The story begins with a young boy named Dan who has never lost a Bakugan match. While in a match against a bully Dan sees a vision of two Bakugan brawling. Is there more to the game than what the players think?

A mysterious Bakugan player named Masquerade, who is ranked at #1 on the list of Bakugan players, is stealing Bakugan from players worldwide. Dan makes an open challenge to Masquerade, and loses two of his Bakugan to this mysterious player, thanks to a Doom Card, which makes a Bakugan disappear forever. Dan is lucky enough to not lose Drago, but might if he loses to Masquerade again.

Masquerade teams up with a player with Rikimaru, by giving him a very special Bakugan. When Rikimaru and Dan battle, Drago ends up using a dangerous move to save himself and win the battle. Dan gets angry, and throws Drago into a river, cursing the day they met.

Dan has a hard time adjusting to life without Drago. He ends up causing a schoolmate named Ryo to drop his computer and runs away, hurting Ryo's feelings. Masquerade takes advantage of Ryo's hurt feelings, and Ryo beats Dan in a battle. Dan finds Drago, and tries to make up with Ryo.

Dan and Runo meet for the first time, outside of the Bakugan website, and realize that they live in the same town. Dan drops his BakuPod, and Runo picks it up, noticing that Dan has battled Masquerade. She goes in his place, but ends up battling a boy named Tatsuya.

While at an amusement park, Dan and Runo are invited onstage to assist a magician act by two brothers. Dan picks a card, and realizes it's a Doom Card. The brothers are working for Masquerade, and Dan and Runo get tricked into a battle.

Marucho reveals that he secretly moved to Dan's neighborhood, and throws an elaborate welcome party. Masquerade makes a business offer with the famous pop band duo, Jenny and Jewels. The duo crash the welcome party, and challenge the Battle Brawlers.

Dan and Marucho fight against the pop star duo, Jenny & Jewels. After a narrow victory, Drago tells the Brawlers about how the Bakugan came to Earth, and how a human entered the Bakugan world of Vestroia.

Masquerade manipulates two boys, Kosuke and Takashi, into using his Doom Cards against the Bakugan Battle Brawlers. He promises that he'll reunite their friend Ai with her brother if they help him. Wanting to help their friend, they take the bait and soon run into Runo and Marucho, who are at the airport to pick up their website friend, Alice. Luckilly, Alice is skilled in the finer points of combination battle, and coaches her friends to victory. Alice has a secret, however, that might just ruin her friendship with the Brawlers.

Julie and her childhood friend, Billy, go one-on-one in a Bakugan battle. Although Julie's defeated by Billy, she's impressed with his skills and his Bakugan, "Cycloid." They make a great team, and Julie wishes she could befriend a talking Bakugan. Later, when Julie admits to herself how lonely she really is, the Bakugan Gorem appears. The two seem to be destined for each other.

Marucho and Runo realize that the combined powers of the Bakugan Brawlers are not enough to defeat Masquerade. Without Dan's knowledge, they visit Shun to try and get him to join. Shun's grandfather tries to get them to leave, but Shun makes a deal. If they win, he joins. If they lose, he'll walk away.

Alice realizes that she may have a connection with the mysterious Hal-G, but doesn't have the courage to tell the other Brawlers. Meanwhile, Dan recalls the last battle he had with Shun. Shun's mother gives Shun a Bakugan, "Skyress", to watch over him.

Masquerade has been destroying the Bakugans of kids all over the world, and the Brawlers have to put a stop to it. Reluctantly, Dan accompanies Runo and Marucho to Shun's house to recruit him one more, but find out he's joining Masquerade! Dan accepts the challenge of battle, and with Drago, fights against Shun and Masquerade.

Lured by an invitation to celebrate their world class rankings, five of the top ten Bakugan players gather at a mysterious mansion. There they meet Masquerade & the evil Bakugan "Naga". They're put under a spell to take Dan & the other Battle Brawlers out of the picture. Meanwhile, Alice confesses that she believes that her grandfather Michael is responsible for the destruction of Vestroia. They decide to take a look around Michael's lab to find evidence of what happened to him.

The Brawlers finally meet Julie up close and personal, but the mood goes from happy to sad when they see what's happening in Vestroia. Julie and Shun fight with Julie's friend Billy, the 9th ranked Bakugan player, and her neighbor Komba, the 5th ranked Bakugan player, knowing they were tricked by Masquerade to take out Dan and the rest of the Brawlers.

Julie is still upset about Billy's betrayal, but tries to put it behind her so she can support the other brawlers. Meanwhile, Shun tells them about a valley similar to Bakugan Valley. Everyone heads there but on the way it is revealed that Shun lied about it being similar, and it was all a ploy to try and see why Masquerade always knows where they are all the time. He tells them that there has to be someone spying on them. At the valley, the 3rd best Brawler Chan Lee appears and challenges Dan to a brawl.

The Brawlers are having trouble finding the Infinity Core. When they learn that their location might be being broadcasted, they shut off their signal.

When Marucho loses his Bakugan to Klaus, he and Runo give chase, and wind up in Masquerade's castle!

After a quarrel between the Brawlers, they all go separate ways. Julie decides to pursue her friend Billy and try to save him from Masquerade's evil ways.

When Shun leaves the group, Alice chases after him. Meanwhile Dan goes to take on Masquerade alone.

Klaus, Chan-Lee, and Julio return to finish off the Brawlers. Dan, Runo, and Marucho take them on, but what will happen when Klaus uses Marucho's stolen Bakugan?

The Brawlers have been pushed back, but will the return of Preyas and the evolution of Drago be enough to bring them to victory?

Learning that Webmaster Joe is at the hospital, Dan and the other head there. However, while heading for Joe's room, Drago gets lost.

Alice helps a little boy defeat his biggest rival.

Tensions form between the group of Brawlers when it is believed that one of them is a double agent.

The Brawlers head to face Masquerade in one final battle.

The Battle Brawlers learn through Webmaster Joe (who was on a trip with his mother) that Masqerade has defeated the World's Top Bakugan players, so they try to come up with a strategy to beat him. The strategy seems to backfire when Masquerade visits Dan's house and gets him to accept a battle. Now the evolved Drago and the evolved Hydranoid will go head-to-head with the loser getting a one-way trip to the Doom Dimension, which is later revealed to be full of Bakugan turned into stone.

The Brawlers mourn over the loss of Dan and Drago. Meanwhile, Shun gets a challenge from Masquerade and decides to join Dan in the Doom Dimension. When Skyress learns of this plan, she tries to gather the other Bakugan and try to save Vestroia without putting their human partners in risk. Soon, the other Brawlers catch onto his plan and decide to join him, but first Runo makes a promise to Dan's mom - he's safe and will be home soon.

In the Doom Dimension, the Legendary Ancient Warriors of Vestroia prepare to test the powers of the Brawlers, seeing if they are worthy enough to save Vestroia. The Brawlers are separated and Julie is left with Gorem to face the Subterra Warrior, Clayf, and a shadow of her perfect sister, Daisy. With help from Gorem, Julie learns that she isn't her sister and she can only do the best she can do. Because of this, Gorem evolves into Subterra Hammer Gorem, and defeats Clayf.

Marucho must battle the Aquos Elemental Warrior, Frosch, and he is forced to send in Preyus early when he learns he is battling a shadow of himself. Preyus isn't feeling well throughout the battle, but he is able to give Marucho guidance to accepting his past. Marucho knew that he only did what his parents told him to make them happy, but he didn't like to always be so obidient. This causes Marucho to hate his old self. By accepting the past him, Marucho was able to help Preyus' digestion problem. This allows Preyus to evolve by spitting out his brothers: Aquos Angelo/Aquos Diablo Preyus. Will the combined strength of these brothers prove to be enough to defeat the Aquos Warrior?

Shun is stuck with the female Ventus Lord, Oberus, who has summoned a child that looks like Shun's mom to battle. The child convinces Shun to play with her while the sun is still setting, which it never does. Shun must battle himself as well when he is forced to choose between going back or staying in this world with his mother. In the battle with Oberus, Shun believes that he doesn't need his friends. His belief causes Skyress to die after a great impact with Oberus. When Shun realises his mistake, a tear drops down onto Skyress' ability card, changing it, and miraclesly reviving Skyress, which evolved into Storm Skyress. In the end, when Shun chooses to return to his world, Skyress evolves to Ventus Storm Skyress.

Runo and Tigrerra must battle a young boy from Runo's past (a smaller version of Dan) summoned by The Haos lord, Lars Lion. The test is for Runo to realize how much she truly treasures her and Dan's friendship/love. When Tigrerra is getting hit by Lars Lion's piercing arrows of light, Runo realises the friendship/love that she treasures and says "We are Friends Forever Dan!" in the English dub, while she says "I love you Dan!" in the Japanese Version. When Runo realizes this, Tigrerra evolves into Haos Blade Tigrerra.

Dan must battle the Pyrus Lord, Apollonier, in order for him and his friends to return to their world. He and Drago soon find out that they're battling a clown. Dan manages to win the battle, but Drago doesn't evolve. When Dan rips off the clown's mask, it turns out to be Runo. In order for Drago to evolve and Dan to past his test, he must battle, and win, against each of the Brawlers.

Joe is determined to find out where his friends have gone, so he challenges Masquerade to a battle. At first Joe appears to be outmatched, but Wyvern returns to give Joe assistance. The Brawlers also return, and Masquerade realizes his battle is only beginning. Dan explains everything about the Bakugan to his mother, who believes him and asks Drago to take care of him. Naga is revealed as one of the most dangerous Bakugan in the world.

Dan tells Shun, Julie, and Marucho that he has yet to pass the test in the Doom Dimension and the only way to have Drago evolve he has to defeat his friends one by one. Julie first battles Dan and Dan wins. Then, he battles Marucho and wins again. Shun says he will battle Dan the next morning. Masquerade is in the Doom Dimension and is about to start a battle with Alice.

Dan's final test is to beat his friends so his Dragonoid can evolve to the next level and become the Ultimate Bakugan. Dan battles Runo and Shun while Masquerade goes to see the Darkus Lord, Exeedra, and he ends up fighting Alice as a mirage.

Joe shows up after Dan defeats Julie, Marucho, and Runo for Wyvern to check out Drago's battling skills when Dan and Shun have their battle to finish Dan's test. Meanwhile, the Darkus Lord and Masquerade finish their battle. In the end Drago beats Skyress and becomes the Pyrus Ultimate Dragonoid, and Duel Hydranoid beats the Darkus Lord and evolves into the Darkus Alpha Hydranoid.

Alice appears to be disappearing all the time. Dan goes to talk with Marucho, Runo, Shun, and Julie and ends up finding Alice! Alice won't explain anything and leaves. Later, Joe receives a message from Masquerade, and Dan decides he'll take over to fight Masquerade with Drago to end it once and for all with Masquerade. Dan wins and offers Masquerade to join the Battle Brawlers to help defeat Naga. But Masquerade refuses and takes off his mask. It is revealed that Alice was Masquerade the whole time!

Hal-G appears to explain the origin of Alice and Masquerade. Because she is unable to forgive herself, Alice then disappears. Meanwhile a huge hole opens up in the ocean and weird weather has been happening all throughout the earth. Through much convincing, the Brawlers convince their parents about the Bakugan. What will they find in the decaying Vestroia? Dan and the Brawlers decide to take a little road trip, to Vestroia!

Alice tells Klaus about what she did as Masquerade, and gets pulled into a battle to punish her for sending his Bakugan to the Doom Dimension while she had been Masquerade. However, Klaus was just trying to teach her a lesson, that everyone, and everything must work together in order to create harmony.

The Bakugan Battle Brawlers enter Vestroia and realize Vestroia has become a hybrid world where two elements are mixed together to make one element together. They enter the Ventus and Aquos world where they meet Tayghen and Hairadee: two Bakugan of both Ventus and Aquos elements. As they fight, they suddenly see the portal to the next hybrid world of Vestroia is closing and so they agree that Shun and Marucho are to stay in the Ventus and Aquos world to defeat the two Bakugan. The rest of the Bakugan team disappear through the portal into another dimension of Vestroia.

As the remaining Brawlers enter the hybrid world of Subterra and Haos, a pair of Subterra/Haos Bakugan sisters named Rabeeder and Tricloid fall in love with Dan. The sisters say the only way out is if they beat them in a race. Dan and Drago win and leave to the next world.

Dan and Drago enter the hybrid world of Pyrus and Darkus where the dark army is running rampant. Dan and Drago are saved from Pyrus/Darkus hybrid Bakugans Centorrior and Druman by Nobilion: a Pyrus Tigrerra who is the oldest and wisest of all Bakugan. Nobilion explains how the negative energy has been influencing all of Vestroia, except those who can hide. Nobilion also mentioned that the Negative Energy has also created the evil hybrid Bakugan. Upon running into Centorrior and Druman again, Drago and Nobilion end up engaging them in battle. With Nobilion's sacrifice, Dan and Drago try to defeat Centorrior and Druman.

Alice arrives in Vestroia as Masquerade in order to help her friends. Masquerade finds Dan and he begins to help the weakened Dan and Drago. Centorrior and Druman though are able to counter sound judgment and all the power-ups that their Bakugan are given. Dan and Masquerade must work togerther to defeat Centorrior and Druman alongside an army of Serpenoids and Gargonoids. With Masquerade and Hydranoid using a cut and run trick, Dan and Drago lure them to the right spot where Hydranoid's attack manages to defeat Centorrior. Drago then uses his attack to defeat Druman. Masquerade then fades away encouraging Alice to continue on being a Bakugan Brawler and Alice obtains Hydranoid in the process. When the Brawlers reunite with each other, Centorrior and Druman watch from afar and stated that they are together just as Naga planned it to be.

The Battle Brawlers have managed to unite each element together, and they are given the blessing as the six new warriors. Hal-G and Naga are still causing chaos over Vestroia though, and now they are attacking Earth with the help of the hybrid Bakugan (Taygen, Hairadee, Rabeeder, Tricloid, Centorrior, and Druman) leading their Bakugan armies. The Brawlers must figure out how to save both worlds. Help is on the way though. Chan Lee, Billy Gilbert, Komba O'Charlie, Julio Santana, and Klaus Von Hertzon lead every Bakugan players of the world when they have decided to give assistance. Once Naga starts attacking with negative energy, his minions get charged up to turn the tables against the Bakugan players. Joe contacts the Brawlers that Naga in the real world. Drago senses Wayvern is in trouble when he sends his minions to find the Infinity Core, so the Brawlers head back to take on Naga.

Wayvern puts up an energy shield around Wardington powered by the Infinity Core to hold off Naga and his troops. Meanwhile the Brawlers return and join in the battle to protect all of Earth and defeat Naga before he can join the two cores together. Failure means that both worlds will be destroyed. Jenny, Jewels, and Marucho protect the city via sea, where the Ventus/Aquos hybrid Tayghen has been creating tsunamis. The singing of Jenny and Jewels gets Bordington's fans to come out and cheer. Can Marucho, Jenny, and Jewels defeat Tayghen?

The battle against Naga's troops continues as Julie and Billy team-up to take on the Subterra/Haos hybrid Bakugan called Tricloid, who has been powered up by Naga negative energy. At first the two seem to be overpowered, but the adaption of each other's battle styles may be what's needed to help them realize how to work as a team again, especially when Naga decides to crash the party. Shuji and Akira also appear trying to get strategies from their sister Nene. With help from Nene and her Ravenoid, Gorem and Cycloid defeat Tricloid by getting rid of the Negative Energy that Naga placed on her. At the end, Julie asks Billy out on a date.

Naga's troops have finally infiltrated Wardington after two defeats. Alice discovers that Tricloid's sister Rabeeder is invading the town. Little does she know the one she trained, Christopher, will also get involved in the battle. Dan is informed that Hairadee, Centorrior, and Druman are also approaching the city following Tayghen and Tricloid's defeat. When it appears these two are being overpowered, Klaus arrives. The three soon realize all that Rabeeder is doing is being controlled by her worry for her sister Tricloid. Alice starts doubting herself but Christopher helps her. Hydranoid defeats Rabeeder and is reunited with Tricloid as both of them return to Vestroia.

The return of Naga's Ventus/Aquos servant hybrid Hairadee has brought new troubles for Komba and Shun. While Skyress is trapped in a barrier of ice, Shun reveals his ninja skills to free Skyress and defeat the hybrid. Julio crashes the party and helps the battle. Will the three of them be enough to take Naga's servant on?

Dan and Runo stand as the only defenses against Centorrior and Druman. As Dan recalls his past battle with them, he realizes they don't have a chance without help. Julie, Billy, Marucho, Klaus, Julio, and Komba also get involved in the battle due to Hal-G doing a blurred transmission by Hal-G posing as Kato. Elsewhere Alice stands ready to help her grandfather, Hal-G, who appears to have fully become himself again. She takes him where Joe and Wayvern are. It's all a trick though. He unleashes Naga. Shun has suspected a trap though, so he shows up and fights Naga. When Joe gets captured, Chan-Lee frees him and joins the cities last line of defense by unleashing Fortress. While Drago is stuck battling the last of Naga's servants, Wayvern is in great distress.

Wayvern is calling to Drago to tell him that she needs help, the top ranked Brawlers must defeat Centorrior and Druman. Meanwhile Naga's negative energy is proving to be too much for Wayvern and Fortress. With Centorrior defeated, the others deal with Druman as Dan and Drago head over to where Naga. When Drago arrives, he fights Naga. With help from Julios, Runo has Tigrerra destroy Druman. Wayvern asks Drago to attack her so she can give him the Infinity Core. He does so, and Wyvern disappears. Drago becomes Infinity Drago. Drago then continues his fight with Naga. They both have 1000 Gs. In an epic battle, the two seem evenly matched. However, Hal-G sends out his 5th Paladins to assist Naga.

As Hal-G releases 5th Paladins, all seems hopeless until the Brawlers send their Bakugan to aid a wounded Drago. They destroy the 5th Paladins as Naga absorbs the 5th Paladins' energies. With the last of his power, Drago fires a brilliant burst of fire.

The peace of New Vestroia does not last long. A race called the Vestals invade and colonize New Vestroia, turning the Bakugan back into balls and making them their slaves for amusement, not knowing that Bakugan are intelligent creatures. One by one the six fighting Bakugan are captured leaving only Drago. In an effort to stop this, Drago is separated from the core of Vestroia by the six legendary warriors, and heads to Earth to seek out Dan Kuso, and the two leave for New Vestroia, with Marucho following after overhearing Drago's plan to leave the others behind. After they learn that the Vestals are responsible for the state New Vestroia has fallen into, he challenges Lync Volan and Volt Luster, two members of the Vexos. A Vestal named Mira, part of the Bakugan Brawlers Resistance, interrupts and tells Dan of the new brawling style required for Bakugan battles. Dan manages to adapt to the new method quickly and wins two Bakugan from Lync and Volt.

After the battle with Lync and Volt, Dan, Drago, and Marucho go with Mira to the Resistance base. Along the way, Mira reveals that only a few people of the Vestals realize that the Bakugan are intelligent creatures, while the rest of the people have not been told. She reveals that after discovering this for herself, and becoming outraged with her father for participating in the capturing of the Bakugan, she ran off and created the Bakugan Brawlers Resistance, joining with people who thought as she did. Upon arriving at the base, they meet Baron, a major fan of the Bakugan Battle Brawlers and the 6 hero bakugan. Shortly after, another Resistance Brawler named Ace, highly disapproves of Mira bringing humans to aid in their quest to free the Bakugan. Instead, he challenges Dan to a battle, and says that if he beats him, he and Marucho can join the Resistance in their quest to save the Bakugan. Dan gets off to a rocky start, but he and Ace are too evenly matched. With one win and one loss for each their battle ends in a tie and they become fast friends.

Now that Dan and Marucho are part of the Resistance, they gear up and get ready to fight back against the Vexos, first by heading for Alpha City and the Alpha dimension controller, the machines trapping bakugan in their ball form, to take it down. To get themselves ready, Dan offers to train Baron, whom gladly agrees and can't wait for the lessons to begin but is afraid what will happen when Dan finds out that he was the one who lost Tigrerra to Spectra. But after Lync and Volt were defeated, Spectra Phantom sends out Mylene Pharoah and Shadow Probe to ensure that the Resistance is taken care of. The next day, in the middle of his training, Baron reveals he is discouraged after losing Tigrerra to Spectra in a battle, and says he isn't worthy of the lessons. Just then Mylene and Shadow crash land and Shadow is forced to battle Baron. After losing before, Baron is discouraged and is afraid of losing Nemus the way he lost Tigrerra. But, on the brink of losing Nemus for good, Baron pulls through and wins back three of Shadow's bakugan.

Seeing how desperately he needs a partner to help Dan and the Resistance, Marucho takes his gear and heads out, in search of a Bakugan to battle with. At the same time, Mylene also goes hunting for Bakugan, after throwing away three she claimed useless. In the morning, Marucho meets Aquos Elfin, a Bakugan who turned out to know and have what might be a crush on Preyas. She explains that after his capture, she had to watch over the forest and protect the Bakugan living there from any harm. When Marucho asks to be partners with her, she at first declines because she claims to be "waiting for the right partner". But when Marucho explains that he needs her to help free the Bakugan (as this was what Preyas would have wanted) she says that if he passes her test, she will at least think about a "temporary partnership". As the testing goes underway, with Marucho not doing so well, Mylene flies over, and in fury, Elfin and Marucho demand she and the Vexos return the stolen Bakugan. Angered at how cruel Mylene is to the Bakugan she already carries (by throwing them away like trash), Marucho and Elfin challenge her to a brawl. But Mylene soon begins to show her skill, and may end up winning Elfin as a new Bakugan! just when all of mylene's bakugan were no use, she unleshed a bakugan called a bakugan trap. Just when Mylene is about to seize Elfin, a hooded figure wielding Ventus Bakugan arrives and saves Marucho. Mylene states she's tired of losing to this hooded person and offers him to join the Vexos, but he leaves without saying a word and Mylene departs. Meanwhile, Marucho slowly awakens, despaired that Elfin was gone. But as it turned out, Elfin was merely off to find him some water, and then begins explaining how she couldn't let anything happen to her "goofy partner". In the end, Elfin and Marucho are partners, able to aid the Resistance in their journey. Later, in episode 6, it is revealed that the hooded figure is Shun.

With the Vexos losing one by one, Gus Grav calls them all together to explain that the Resistance has to be defeated. So Gus decides to take matters in his own hands and confront the Resistance, and bring pride back to the Vexos. Meanwhile, the Resistance makes a stop en route to Alpha City, where Mira gives Dan a Bakugan Trap called Scorpion to help in his battles. Not much is known about the Trap Bakugan except that they are incapable or unwilling to communicate. Excited, Dan takes off to get in some training with Scorpion. Just then, Gus shows up and starts to mess with Dan's head, asking what he will gain from saving the Bakugan, leaving Dan with this question. He returns later, asking Dan what the answer is to his earlier question, and it is revealed that he is the number two brawler among the Vexos. Feeling confident, Dan decides to take him on, but is soon overwhelmed with the power of Gus' Bakugan Subterra Primo Vulcan.

When Prince Hydron is furious because of his incomplete collection, Spectra and Gus challenge Dan to a battle in an effort to catch Drago. While the Resistance plans to attack Alpha City, Mira wants to take a short detour to find her brother. It is hinted in this episode that Ace starts to like Mira, during in the arugment, he seems and sounds like that he was worried about her going somewhere that might be dangerous. In the midst of the argument, Dan sneaks away with Drago to fight Gus and manages to battle well until Spectra joins in and Dan starts to struggle in the fight. Out of nowhere, Shun comes to his rescue. Shun beats Gus and Dan beats Spectra when Drago displays a massive power surge due to Helios' taunts about Tigrerra. Seeing that huge amount of power Spectra shows hint of betrayal when he said that he won't let the magnificent Bakugan become a play thing, meaning that he won't give it to Prince Hydron if he captures it. Back at the base, Shun explains that while he was in the mountains a portal opened up right in front of him and got sucked through to New Vestroia. After he rescues Ingram from the Vestals, she remained in his debt and the two banded together to free the Bakugan. As they make their way closer to Alpha City and the dimension controller, Dan asks why Shun didn't reveal himself earlier when he rescued Marucho. Shun explains that he had something important to attend. When they approched Alpha City, Shun revealed he'd break in the city and find his Skyress.

After Shun successfully leads the Resistance into Alpha City, Mira departs on her own mission: searching for her older brother, Keith. She heads to her home to search for clues on her brother's computer but comes up with nothing. After her father, Dr. Clay, arrives, she confronts him and he simply says that "He is no more." When she further questions him, he leaves for his lab, while Mira follows. Meanwhile, Shun takes the others to check out the control spire and they learn that the battles that take place in the arena below the controller are synchronized with the controller's power. At the lab, Mira witnesses the birth of the first cyber Bakugan: Altair. As the boys make their way to her location, Mira is confronted by Lync, who is armed with Altair. During the battle, Mira seems to have the upper hand with Wilda and her trap Baliton. That is until Lync activates two Double Abilities in a row. The scientists are worried about Altair's power fluctuation but Dr. Clay orders Lync to destroy Wilda and Baliton. Before he can, the massive overload causes Altair to crash and shut down, ending the battle. Dr. Clay decides to use the data to perfect Altair into the most powerful Bakugan ever.

Ace and Shun team up in a Bakugan battle tournament in order to overload the dimension controller because it draws power from bakugan battles. After Marucho is disquaified in the singles round, he sneaks the others in. They almost get caught by some guards until Mira pretends to be a huge Vexos fan and they manage to slip away. As they remain hidden, the Vexos show up and Mira notices that Spectra tosses his Bakugan the same way as her lost brother Keith (later realize that Spectra might have somthing to do with the disappearance of Keith). Meanwhile, Ace and Shun are having trouble getting along in the battle tournament and are starting to lose against the Dark Angels who are Vexos wannabes. When their opponents begin taunting them, Shun and Ace put their differences aside and finally come up with a plan. They win with ease while claiming their opponent's Bakugan. Shun and Ace prepare for their match against Lync and Volt.

Shun and Ace have made it to the finals and they prepare to battle Lync and Volt. they were brawling with altair and volt's new bakugan, brontes. Meanwhile, Dan and the others head to the dimension controller, but lose Marucho on the way! Things only get worse when they discover many other talking bakugan and then they are captured by guards who are marveled by the speaking Drago. Just then Marucho drops in and saves them. Things get worse for Shun and Ace when Lync combines his Ventus Altair with Ventus Wired and their bakugan traps seem to have no effect. Shun and Ace discover Altair's weakness: it cannot sense multiple opponents and they manage to destroy it. While the others hold off the guards, Dan makes his way to the controller, finding that it is guarded by lasers. He throws Drago through the lasers and he hits the reverse switch, destroying the controller just as Shun and Ace defeat Lync and Volt. The newly freed bakugan rise up from the ground and everyone in the stadium learn the truth about the bakugan.

As the Resistance heads to Beta city, Runo decides to go to New Vestroia to help Dan. After Kedo flies her and Julie to Moscow to meet with Alice and her grandfather, Dr. Gehabich reveals that his transporter is not functioning properly and refuses to let Runo go. Later that night, Runo and Julie sneak into his lab and Julie prepares to send Runo off. Meanwhile, in New Vestroia, everyone is beginning to hear their conversation because of the weakening wall between the two worlds. Runo does make it to New Vestroia but finds that she is only half way there, being unable to touch anything {she trys to hug Dan} but still able to see and speak with Dan. Prince Hydron decides to take advantage of Runo's distress by sending Shadow to make sure that Runo remains trapped. While Marucho handles Shadow, Dan takes Runo to the gate only to get attacked by Shadow's bakugan. With Dan down, Runo rushes to help him but he urges her to go to the gate. To make matters worse, Spectra, Gus and Lync follow her through the portal as do Dan, Mira and Baron.

Dan, Runo, Mira and Baron make it to the human world but pick up some unwanted visitors: Spectra, Gus and Lync! Marucho manages to defeat Shadow and he, Shun and Ace decide to take out the Beta city controller to pass the time. Before Spectra takes his leave, he grabs Runo as a hostage and offers Dan an ultimatum: join the Vexos or risk Runo's safety. Dan, Julie, Baron and Mira split up and Dan and Julie run across Spectra and Runo. Mira chases after Gus to find Spectra and Baron fights Lync. Spectra reveals that he is actually against Prince Hydron's rule and wants to team up with Dan to take him down and in a show of good will, releases Runo. Mira's suspicion of Spectra being Keith only rise as she believes that he infiltrated the Vexos to free the bakugan. After Baron defeats Lync, we learn that Spectra and Gus only want to take down Hydron so that Spectra can succeed the role of ruler of the Vestals. Meanwhile, Dan refuses to believe Spectra intentions and before anything happens, Alice warps in using Masquerade's warp card. She takes Spectra and Gus (and Dan) back to the lab where Dr. Gehabich sends Spectra and Gus back to New Vestroia. Unfortunately, the transporter must be repaired before another trip can be made. So, Dan takes Runo, Julie, Mira and Baron to his house for the meantime. Lync crashes in but refuses Dan's hospitality but accepts Alice's, due to his hunger, after their ride leaves. Alice doesn't like Lync one bit and tells him that when the transporter is repaired, he is "so gone". Before the credits role, Lync is seen crying after Alice leaves him some food.

Mira and Baron are stuck on Earth so Mira decides that they need to take a break so they go to an amusement park. Mira and Julie are separated from the rest of the group and run into Spectra and Gus who say that they came back to Earth by tracking down Dan's Gauntlet to the amusement park. Mira wants to know if Spectra is her brother Keith so she decides to brawl against him. However, Gus rearranges their little deal so she battles Gus instead. If she wins, Spectra takes off his mask but if she loses, she has to join Vexos against Prince Hydron. At first Mira struggles against Gus' abilities, but with help from the original Subterra master Julie and her copycat ability card, Mira pulls through and defeats Gus. Despite Gus' attempts to dissuade Spectra, he removes his mask and is revealed to truly be Mira's brother Keith.

While Mira and Baron help out at Runo's family's cafe, Ace, Shun and Marucho head to Beta City to shut down the controller, which has grown stronger due to Drago (and the Perfect Core's) absence. Hydron sends Mylene to deal with the resistance in Spectra's absence and states to himself that, when he returns, Spectra will find that the Vexos have a new leader. Later at night, Ace, Shun and Marucho hear the voices of Mira and Dan (respectively) and head out into the night. But it turns out that Shadow is the one making the fake voices. By the time Shun realizes it's a trap, Marucho and Ace fall for it. Ace wakes up in another place and finds Mylene. realizing that he has fallen for a trap. Ace begins struggling to defeat Mylene and her new attribute changing bakugan, Elico. In a flashback it is revealed that Ace is rumored to be a top brawler possibly stronger than the Vexos but refuses to enter tournaments. Mira confronts him and asks him to join her team. After he lost to her, she gave him Percival and he learned the truth about Bakugan. Back to Ace's battle with Mylene, Ace becomes submerged in water and loses to Mylene...and he does not arise, he is lost.

Marucho finds himself in a desert with Elfin. After falling into quicksand, he is rescued by Volt who later engages him in a battle. Marucho seems to be doing well with his new trap, Tripod Epsilon but when Volt pulls out his trap, Dynamo, things get rough and Marucho is defeated. Back on Earth, Mira and Baron hang out at Dan's, who after waking up from a dream, is still eager to return to New Vestroia in order to help Shun and Marucho.

With Ace and Marucho captured by the Vexos, Shun decides to head to Beta City alone to destroy the controller. On the way he is ambushed by Shadow Probe who is armed with Darkus Hydranoid! In the middle of the battle, Shun and Ingram realize that it is not the same Hydranoid they know, it is really mechanical bakugan Darkus Hades in disguise. Darkus Hades was created from Hydranoid's DNA and has none of the weaknesses that Altair had. Shun tries his best to hold his ground by Ingram and Hylash are no match for Hades and Bakugan Trap Darkus Fortress. Shun contemplates throwing in the towel out of fear for losing his partner like how he almost lost Skyress in a tough battle, but Ingram convinces him otherwise and that he will always be there. Shun is defeated by Shadow and passes out. The Vexos, having now captured the rest of the Resistance, plan to keep them as hostages while keeping Dan and the others stuck on Earth forever and while they take all Bakugan.

Spectra and Gus, stuck on Earth, stay in an abandoned factory. When Gus returns with "juice in boxes",(there's no such thing asjuiceboxes on Vestal) he finds that Spectra is gone. While Dan trains Baron, Spectra runs into a fortune teller who tells him that if he stays on the path he's chosen than he will meet his end, but Spectra does not listen to her. Spectra decides to take Drago by force, now being tired of waiting for Dan to join him. He sends one of Gus' hornets to challenge him and they meet in the arena where he last fought Masquerade. Mira, Baron and Runo worry about Dan being out on his own. In the first round Dan takes a major loss, but manages to strike back with Pyrus Scorpion. But then Spectra pulls out his own mechanical Bakugan Trap Pyrus Multisided Metalfencer. Helios gets frustrated and demands that Spectra gives him more power. Spectra willingly obliges and activates a forbidden ability card to give Helios absolute power. Dan and Drago are disgusted by this massive power and what it could do to Helios, but neither Spectra nor Helios seem to care about the consequences. Drago is no match for this power and loses, with Spectra claiming him as his prize. Dan is crushed by his defeat and the loss of his partner while Spectra walks by the same fortune teller who is shocked by how much darker his future has become. Once again, Spectra does not care.

Dan is upset about losing Drago but tries to move on and think of ways to get him back: starting with all out intensive training. Meanwhile on New Vestroia, Mylene wants to close to portal to keep Dan and the others on Earth, but Prince Hydron orders her not to, so as to allow Spectra and Gus time to return, which angers Mylene, who greatly enjoys her new power. Apollonir states that they must retrieve Drago as the Perfect Core is losing power and the other two dimension controllers are growing stronger. While training, Dan faints and develops a fever. He runs out into the park calling out to Drago, lamenting over how he lost Drago. All of a sudden, Apollonir shows up and to retrieve Drago, but Dan regrets to inform him that he lost Drago. Apollonir is disappointed that Dan has given up so easily and suggests that Drago is also upset at himself for losing the battle and letting Dan down. Dan wakes up, with his fever broken, to find that Apollonir has crossed over to Earth. Apollonir, linked to the Perfect Core like Drago, and is easily able to find Spectra and teleport everyone there. Spectra accepts Dan's challenge but brings out Helios to test if Apollonir is worthy of fighting Drago. Apollonir lectures Spectra on true Bakugan spirit but Spectra believes that power is the only way to win and brings out his Bakugan Trap Metalfencer. However, Apollonir easily takes them both down in one hit. Spectra finally sends out Drago, but Dan is shocked to see his friend has been altered in appearance while under Spectra's control.

Dan, with the help of Apollonir, brawl against Drago, but Drago is not himself any more. Spectra has turned him into a corrupted black dragon. Dan tries to reach out to his friend, but it seems that Drago is unable to listen. Spectra uses the power of many forbidden cards to access Drago's Perfect Core abilities, but it puts Drago under mounds of stress. The legendary warriors conclude that Drago should not have been able to access the Perfect Core's power and change attribute while in his new body, but the power of the forbidden cards allows him to do so. Things look bad for Apollonir, as Drago seems unstoppable with all this power. Dan then notices that Drago is crying and that if he doesn't stop Spectra from giving Drago so much power, Drago could die. Apollonir believes that the only way to help Drago is to transform himself into pure energy and enter Drago's body to absorb the extra energy, however, Apollonir will not be able to attack or defend himself. Also, Dan must throw Apollonir into Drago's chest, but if he misses, Drago's condition could worsen and Dan may end up killing Drago and New Vestroia may turn back into six separate worlds. Dan successfully launches Apollonir into Drago's chest and Drago falls, defeated, returning to his normal self. Dan and Drago are happily reunited while Spectra does not seem that affected by the loss, and only insists that things will be different the next time they meet

The Resistance is ready to head back to New Vestroia and Dan wants to bring Runo, Julie and Alice along. But Mira suggests that they spend one last day for Dan to say goodbye to his parents. Alice uses her teleportation card and Lync convinces her to take him too, but he really just needs to meet up with Spectra and Gus. As Dan and the others meet Alice at the tower, Apollonir opens a portal to New Vestroia. However, they are ambushed by Spectra, Gus and Lync and to make matters worse, Mira betrays them and heads into the portal after explaining that Spectra is her brother. Dan and the others miss their chance and Apollonir is not strong enough to open another portal, so Alice takes them back to Russia to use her grandfather's transport machine. But, because Dr. Michael used the technology in Lync's Gauntlet to repair the machine and only those with Gauntlets can go through, meaning that Runo, Julie and Alice must stay behind. When Runo lies that she never really wanted to go to new vestroia and lashes out at Dan telling him to never come back he grabs her hands and says how hes sorry she's not coming and they gaze into each others eyes until the machine is ready he slowly lets her hands go. After that heartfelt goodbye with Runo, Dan, as well as Baron head through the transporter.

As Dan and Baron safely make it back to New Vestroia, they find their base completely empty with no sign of Shun, Ace or Marucho anywhere. They discover that they are near Beta City and resolve to head there believing that Shun, Ace and Marucho have gone there. Meanwhile, as Spectra makes his return, the other Vexos are shocked to see that Mira is with him, saying that she has joined the Vexos. However, in her mind, she only wants to find out what Keith is really up to. Also, she discovers that Shun, Ace and Marucho have been captured and are being held hostage. She tries to release them. Dan and Baron sneak into Beta City and battle Mylene and Shadow. Meanwhile Mira is interrupted by Spectra who helps her release her friends, but he tells her that she owes him a debt. As the battle wages on, Baron is defeated defending Drago, who taps into the power of the Perfect Core, defeating Mylene and Shadow easily as well as destroying the dimension controller. Ace, Shun and Marucho reunite with Dan and Baron and they make their leave from Beta City. Later, Mylene accuses Spectra of her loss and the escape of the prisoners but Gus reminds her that she lost the battle, not him. Mira is still left wondering what her brother is up to.

Mira is uncertain of her brother's intentions while in Gamma City. Meanwhile, Ace is unconvinced that Mira has betrayed them due to his feelings for her, but they all resolve to head to Gamma City for the final controller. That night, Spectra invites Mira to dinner where he asks her to join him because he needs her and cannot accomplish his goal without her. Mira is unsure and retires for the night. Later she contacts Spectra asking to battle him and let that decide her fate: if she loses, she will serve him but if she wins, he must go back to being her brother. However, after Helios has volunteered to become a cyborg bakugan after Prof. Clay had collected data on Drago while he was in Spectra's possession. Wilda and Baliton prove to be no match for Cyborg Helios and Mira loses.

Mira and Spectra meet with Prince Hydron, who shows her his collection and later receives a message from his father, who is angered by the destruction of the other two controllers. Hydron then orders Mylene to divide and conquer the Resistance, since she has shown that they are weaker on their own and orders Lync to keep an eye on Spectra and make sure that his new mechanical bakugan is ready for battle. The Resistance arrives and Ace and Baron explain that the controller is underground and is the most powerful. They all head in but encounter Volt. Baron deals with Volt while the others proceed discovering that Gamma City is not a real city but a research facility. All of a sudden, Shadow and Mylene appear and Shun and Marucho step in to battle. Spectra takes Mira to see a team of special mechanical bakugan that he and Dr. Clay had designed themselves that were intended for Hydron but he intends to make certain that they only obey him. Spectra then orders Mira and Gus to use the bakugan to battle Dan and Ace to collect data on Drago and Percival. Meanwhile, the others gain the upper hand against the Vexos. Dan and Ace continue to the controller but encounter Gus and Mira. Ace is shocked that Mira has truly betrayed them and Gus orders Mira to prove that she is loyal to Spectra.

Dan and Ace engage Mira and Gus in battle against their mechanical bakugan. During the battle, Mira seems to be purposely losing. Baron, Shun and Marucho have beaten the other Vexos and arrive in time to see Dan and Ace win, claiming the mechanical Maxus Dragonoid traps.(Baron beats Volt; Shun & Marucho beat Shadow and Mylene). Spectra is furious at Mira's betrayal, claiming that they have even stronger bakugan than the ones Gus and Mira used. Mira apologizes for betraying the Resistance, but they welcome her back into the group otherwise. They next head to the Vestal Palace to free all the original Guardian Bakugan and save New Vestroia for good.

With Mira returned, and the Resistance reunited, Dan and the others head for Prince Hydron's sky palace to free Skyress, Tigrerra, Preyas, Gorem, and Hydranoid from captivity. But before they can even get close enough, Hydron activates another dimension controller, causing the Bakugan to turn back into ball form. Quickly thinking, Shun grabs Mira and Marucho and grapples onto the top of a rising elevator and to safety. Down below, Dan, Baron, and Ace are saved just in time by their Bakugan. But before they can think of a way to get up to the palace, Spectra and Cyber Helios challenge them to a battle. As Dan and Drago struggle to fight back against the power Helios now possesses, Shun, Marucho, and Mira have managed to sneak into Hydron's throne room and discover the bronze statues of the five other Guardian Bakugan, just before meeting face to face with Prince Hydron himself. Meanwhile, Mylene, Volt, and Shadow order Dr. Clay to give them an escape off of New Vestroia, as the energy from the battle between Cyber Helios and Drago could destroy everything around them. Dr. Clay at first refuses saying that it would be treason, when Shadow reminds him he works for the Vexos now. Gus overhears their plan, but before he can warn Spectra, Lync hits him over the head and knocks him into a room, locking Gus inside so he can't tell Spectra of their plan. Back with Dan and Drago, Spectra, having underestimated the perfect core's power, has used the mechanical Bakugan he has to make Maxus Helios, a Bakugan who has all six attributes. Dan tries to use a combination of Ability Cards that tap into the Perfect Core's power, but still can't match Maxus Helios's power. Dan realizes he has no choice but to use the Bakugan he got from his battle with Mira to make Maxus Dragonoid, just as Spectra has again used the other six mechanical Bakugan on Helios. The two Bakugan face each other, preparing for the final battle.

As the battle between Maxus Drago and Maxus Helios rages on, Mylene interrupts Hydron in his collection room by dragging him off. She explains that they are leaving New Vestroia. Hydron refuses at first, being afraid to face his father due to his failure to successfully occupy New Vestroia, but agrees to Mylene's plan to label Spectra as a traitor. Meanwhile, Mira, Marucho and Shun try to activate a machine to reverse the process of Preyas, Gorem, Tigrerra, Hydranoid and Skyress's petrification but are unable to determine the numeric code. Dan and Drago take to the skies to battle Spectra and Helios but the power coming from their battle is far too much and they crash into the palace. Mylene prepares for their departure from New Vestroia but not before tossing out Elico and Brontes, believing that Bakugan with feelings are useless and imperfect fighting machines, since Dr. Clay has already created many powerful mechanical Bakugan. Out of a stroke of luck, Elfin discovers the activation code, but with the palace self destruction under way it may be too late.

As Dan and Spectra continue their battle, and the self destruct sequence begins counting down, the rest of the six fighting Bakugan are freed from their prisons. As Shun and Marucho are reuinted with Skyress and Preyas, the Bakugan in Dan and Spectra's battle suddenly return to ball-like states, and the battle ends in a tie. But CyberHelios wants to continue fighting, even if the battle is over. Cyber Helios and Drago engage just as Ace and Baron, riding on Percival and Nemus, meet up with Shun, Marucho, Mira, and the rest of the six fighting bakugan. As Cyber Helios and Drago battle, Spectra draws a blade, and forces Dan to battle him one on one. Before either battle can reach a conclusion, the Vestal palace explodes, barely giving Dan and Drago any time to escape as Spectra and Cyber Helios retreat with Gus, Brontes, and Elico (whom were thrown out of the escape craft by Mylene). Gus immediately informs Spectra that the others left New Vestroia to blame the occupation's failure entirely on Spectra's betrayal. Spectra merely states that he never really planned on returning to the Vestal home world anyways. Meanwhile, the Resistance celebrates their victory of liberating New Vestroia and freeing the bakugan. Mira, Ace, and Baron decide to return to their world to prevent the Vexos from ever returning to New Vestroia and enslaving the Bakugan again. The others decide to return to Earth with their Bakugan and the original fighting Bakugan, but Skyress declines the offer, saying that she can't bear to leave her home again and that Shun's future lies with Ingram. Right after Skyress leaves, Drago and Dan regrettably inform Marucho and the others that Drago cannot leave New Vestroia, as the Perfect Core is a part of him. But then Apollonir and the rest of the legendary soldiers appear and grant Drago freedom to live wherever he pleases, with the ability to go back and forth between the worlds as he wishes. With that, Dan, Marucho, Shun, and the rest of the Bakugan return to Earth. Various portals open up across the world, allowing Alice and Julie to reunite with their Bakugan. Dan arrives at Runo's family's cafe and tells her New Vestroia has been saved. Just as he believes Runo is about to run to him, she scoops up Tigrerra, reunited with her Bakugan as well. Highly embarrassed, Dan yells at Drago to never speak of this again. Marucho and Shun walk in with their respective Bakugan, and Julie joins the group shortly afterwards. The Bakugan Battle Brawlers are back together again.

Angered by his defeat in Vestroia, King Zenoheld has commissioned Dr. Clay to construct the Bakugan Termination System that wipes out all Bakugan in a predetermined radius. However, the six attributes are needed to activate it. Meanwhile, Mira returns to earth to pay Dan, Marucho, Runo, Julie and Shun a visit. King Zenoheld then challenges the six ancient warriors to a battle for their attribute energy. At first the six ancient warriors are doing great until Zenoheld combines his Mechanical Bakugan and easily overpowers the warriors. In a last ditch attempt, the ancient warriors vanish and summons Drago, Elfin, Ingram, Wilda, Nemus and Percival and their partners to give the six bakugan their attribute powers, causing them to evolve. Dan, Marucho, Shun and Mira wake up to find their Bakugan have truly evolved, and realize that New Vestroia is in danger.

To obtain the Six Elemental Attributes, King Zenoheld has the Vexos search for the Bakugan Brawlers Resistance. Baron, after talking with Ace, decides to move out due to the lack of space in his home occupied by his giant family. While taking his siblings to the park, he runs into Prince Hydron who engages him in battle. All seems well when Nemus pulls out his attribute change ability, but he proves to be no match for Hydron's Subterra Dryoid. Mega Nemus loses the battle and the Haos energy. Baron must find a way to warn Dan and the others about the Vexos' return before they get targeted as well.

While Dan is shocked by a surprise visit from his father and Mira reminisces over Keith, Ace searches the city for a place Baron can stay. As he approaches a future building site for an apartments complex, Baron calls Ace and tells him how the Haos Energy was stolen by Hydron. Then Mylene appears and challenges Ace for the Darkus Energy. As the battle drags on Ace and Midnight Percival eventually become overwhelmed by her mechanical bakugan. Before Mylene can execute the final blow, Sirenoid appears from the lake below them, moments before Klaus, and joins Midnight Percival in battle. With their combined efforts, they manage to drive Mylene away, right after she says she will return with the rest of the Vexos for the Darkus Energy. It is revealed Klaus helped Dr. Michael develop his dimensional transporter system. After meeting up with Sirenoid, his foundation continues to fund the scientist's research as well as managing timeshare on Vestal. By the end of the episode, Baron had arrived to join them and Ace has become frustrated with Klaus's constantly calling him 'boy'.

Klaus, Baron and Ace successfully contact Dan and warn them about the Vexos, so Dan decides to head to Vestal and face the Vexos. However, when Zenoheld decides to test the BT system, Shun heads to New Vestroia with his newly evolved - and now male - Master Ingram, while the others head to Vestal. Once Shun arrives, he finds that all the Bakugan are missing and Master Ingram is still in ball form. Skyress arrives and tells him that a metal sphere came from the sky and sent a beam that trapped all the bakugan in ball form. Shun attempts to destroy the device but finds that it is protected by a force field. All of a sudden, Lync appears to take the Ventus energy and a battle ensues. When Master Ingram and Hylash have trouble against Lync's new mechanical bakugan, Shun is forced to call on Skyress for help. During the battle, Master Ingram begins feeling doubt about his evolution and is taken out of the battle. When Skyress begins struggling against Lync, Master Ingram decides to embrace his new powers and enters the battle, defeating Lync. In the aftermath, Skyress disappears and wishes Shun and Ingram luck.

Mira, Dan and Marucho head to Vestal to meet Klaus, Baron and Ace at Klaus' mansion. It is there Volt comes to retrieve the Pyrus energy after being humiliated by Prince Hydron. Volt and Dan are about to battle when Spectra and Gus appear out of nowhere. Gus attacks Volt psychologically by saying he stole Brontes' soul, as shown in the beginning of the episode. Volt backs away to let Spectra brawl Dan. Mira, Magma Wilda, Marucho and Elfin Version II join in the brawl to help Dan and Drago. In the brawl Dan manages to defeat Spectra after a three minute long battleand using the power Drago received from Apollonir, despite Helios's upgrades. However, before Spectra leaves, he warns Dan that they will meet again.

Spectra makes a false appeal to the Vestals that he is the hero and is trying to stop Zenoheld from ruling all dimensions. On Vestal, Dan and the others purpose to stop whatever he is planning. Zenoheld and the Vexos realize that Spectra has stopped their ability to travel into Vestal by jamming their signals, so Zenoheld sends Shadow to earth to force Dan and the resistance to come to them. Shadow appears and frightens Alice until Chan Lee arrives and the three battle. Alice is initially hesitant to fight, as she might become Masquerade again, but eventually embraces the fearlessness of Masquerade and utterly destroys Shadow's Hades. However, Shadow then reveals his more powerful spider-like Bakugan and wins the battle in one turn. As a result of Darkus Fortress' attack, Dr. Michael's transporter system is destroyed leaving Dan and his friends trapped on Vestal. Meanwhile, Prince Hydron plans to travel to earth to lure Dan and his friends there.

After her loss to Shadow, Alice teleports to Marucho's house to communicate with the Resistance at Klaus' house. She warns them of the Vexos attack on her and that Runo and Julie could be next. Dan decides to head back to Earth, even though it is likely to be a trap. However, since Dr. Micheal's transporter was destroyed, they cannot head back. Luckily, Klaus has one of his own. As the Resistance heads to Baron's house so he can say goodbye to his family, Spectra appears on Klaus' mansion only to find the Resistance are gone and leaves Klaus with a warning. When Spectra returns to his ship, he finds Gus has answered Volt's challenge for Brontes. A battle quickly ensue between the two and Volt tries his best to not attack Brontes directly, causing him to struggle against Gus. When Volt begins to predict Brontes' moves and gain the upper hand, Gus offers Volt a place beside Spectra, but he refuses. Unfortunately Volt is no match for his former partner, loses and passes out. Once Gus returns to Spectra's ship he says that Brontes has served his purpose and tosses him out like trash. Brontes lands on the ground, opens and cries out for Volt to save him.

The Brawlers return back to Earth and see Shun, Runo and Julie waiting for them. In order to evade the Vexos, everyone stays at Marucho's house which is equipped with a shield to hide the attribute energies' signal. Runo gets into a fight with Dan and thinks that he thinks that she's not strong enough to face the Vexos. Runo wanders out into the city hoping to draw in the Vexos, but Mira follows her and they are ambushed by Lync and Mylene. Things go bad and Mira loses her Subterra energy, making the Vexos one step closer to activating the Bakugan Termination System.

After Elfin overhears Preyas talking down about her receiving the energy and rash behavior, Elfin runs off into the city and encounters Shadow Prove and Hydron. Marucho and Preyas arrive in time to rescue her and a battle ensues. At first, Elfin and Preyas have trouble getting along but they put their differences aside and almost defeat the Vexos, but Elfin shields Preyas from an attack and therefore loses the Aquos energy. Preyas, out of anger for Elfin's sacrifice, easily defeats Hydron and Shadow Probe. After the battle Dan, Shun, Ace and Baron fall asleep during the movie that they were watching. No-one else knew Elfin lost the Aquos Energy. The Vexos only need 3 more attribute energies & they can make the Bakugan Termination System, functional.

Baron's little sister, Maron, uses Klaus' transporter to visit Baron, so Julie and Runo suggest to him to show her around town. Meanwhile, Shun sneaks away from Marucho's house an travels to the Samurai theme attraction in the same park that Baron and Maron are at. Shun encounters Volt disguised as a samurai and a battle ensues. At the same time, Baron activates his gauntlet to show Maron how it works and learns of Shun and Volt's battle. The two easily overpower Volt, keeping the Ventus energy safe. Maron bids farewell and thanks everyone for the great day and departs, not before thanking Shun for saving her and kissing him on the cheek.

Billy and Cycloid return to visit Julie only to find that she is at Marucho's house. On his way there, he is unknowingly followed by Mylene and Shadow. Meanwhile, Julie begins showing signs of interest in Ace after spying on him and Dan working out. After insisting she feels nothing for Billy anymore, Julie practically leaps into his arms when he arrives seconds later and introduces him to Mira, Ace and Baron. Billy is apparently caught up with everything happening after running into Klaus a while back and receiving a gauntlet from him. Not long after, Marucho's preparations for a virtual battle chamber called Bakugan Interspace are complete. The system allows anyone from all over the world play Bakugan like a game by logging on to the web. Everyone is eager to test out the machine, except for Shun, saying he has something important to take care of. Everyone draws straws to determine who goes first and Ace and Billy are chosen. Mira and Runo accidentally reveal Julie's crush on Ace to Billy and Ace, not wanting to come between the two, offers to take them both on, which they accept. As the battle rages on, Julie notices that Billy has become much stronger than before after easily defeating Percival. However, Ace easily counters back with the help of his newly evolved Trap Flash Falcon Fly. Meanwhile, Shun checks the security tapes and notices Shadow and Mylene following Billy to Marucho's house. Despite their advantage in numbers, Billy and Julie fall to Ace. After the battle, Shun urges them to return and shows them the picture of Mylene and Shadow from the security footage. Now knowing that the Vexos know where they are, they can no longer hide and wait.

No longer able to hide from the Vexos, the brawlers realize they must now go on the offensive. They plan to storm the Mother Palace and directly attack the Bakugan Termination System instead of protecting the Attribute Energies. But without a working Dimensional Transport system or the coordinates to the Mother Palace, it at first seems there would be no way out for the brawlers. But Dan quickly realizes that they can find the location of the Mother Palace by convincing Spectra. The brawlers are hesistant, as Spectra will not likely be cooperative, and they have no way to contact him. Mira adds that there would be no way Keith would trust any of them. Meanwhile, the Vexos discover that someone has opened a portal to Earth from an entirely different universe. As Spectra makes his way to Earth, Dan and Drago admit how similar they are in both brawling abilities and lifestyles. When Runo interrupts the two for dinner, Dan and Drago are suddenly transported to Spectra's ship now that the former Vexos had broken through to Earth. Once there, Dan learns that Spectra needs the Perfect Core from Drago in order to make Helios the ultimate bakugan. They strike a deal: if Spectra loses, he will take the Resistance to the Mother Palace, but if Spectra wins, Dan must willingly surrender the Perfect Core to Spectra. During the battle Spectra realizes that the only way Helios can defeat Drago is by using his own natural abilities and powerful will to survive and evolve. Eventually Spectra's doubt in himself and his previous methods to perfect Helios leads to his defeat. Dan wins the fight and Spectra agrees to the terms of the bet. Everyone except Runo, Julie and Billy are transported to Spectra's ship, since he states that he would only allow the brawlers and bakugan originally bestowed with the Bakugan Attribute Energies to go with him. As Gus prepares the ship for the transport, Spectra thanks Dan for enlightening him, and refers to him as 'my friend'. Feeling humiliated after his defeat, Helios begs Spectra to make him even stronger. Spectra agrees, saying he will use the data he received on Bakugan evolution from an anonymous source to bring out new powers and new abilities from deep inside the Bakugan.

Spectra upholds his part of the deal to Dan and takes the brawlers to the Vestal Palace, leaving them to find the BT System on their own. Spectra and Gus leave to confront Zenoheld and Spectra tells him to leave the brawlers be. Spectra leaves, but Gus later returns and challanges Zenoheld to a battle to avenge Spectra for being framed and betrayed by the Vexos. Gus' struggles in the battle become more obvious as both Elico and Hexados sacrifice themselves to protect Vulcan and Gus. In the final match, Vulcan protects Gus, saying that his loyalty to Gus knows no bounds like Gus' loyalty to Spectra. The two stand together and take Zenoheld's final hit and fall, dead.

The Resistance split up into groups to cover more ground of the Vestal palace. Shun and Baron encounter Mylene and Volt while Ace and Marucho face Shadow and Lync. At first it looks like things are going well but Dr. Clay uses the palace to send the Vexos' bakugan more power while lowering the power level of the Resistance. Shun and Ace are both defeated and lose the Darkus and Ventus attribute energies. As the others race to find Dan, he and Mira battle Hydron with the Pyrus attribute energy at stake, while Spectra presents a proposition to Dr. Clay.

Spectra offers Dr. Clay a place by his side and the secret to Bakugan DNA, however, Dr. Clay remains loyal to Zenoheld and declares that he and Spectra are no longer father and son. A battle soon begins between Hydron and Dan and Mira, just as Spectra arrives to fight alongside Dan! Mira is quickly taken out just as the others arrive, too late to warn Dan about the Palace sending power to mechanical Bakugan. Spectra brings out his Battle Gear for Helios and easily takes down Hydron, prompting Zenoheld to enter battle. Despite their power together, Zenoheld overpowers them with a last resort power transfer and takes the Pyrus attribute energy, making the BT system fully operational. Unfortunately, Farbros is completely destroyed in the process. With the BT System fully active, the fate of New Vestroia's residents is grim.

With the BT System fully armed, the Resistance and Spectra head to New Vestroia to initiate a mass evacuation. Many Bakugan are sent to Marucho's house on Earth including the Resistance's. However, Drago decides to remain behind to ensure that everyone has been rescued, remarking how many lives have been lost to protect New Vestroia such as Nobilion, Wavern dying, and also the six Ancient Warriors surrending their powers to six normal bakugan. Helios chases after Drago, refusing to allow Drago throw away his life while Helios still has a score to settle with Drago. Drago and Helios agree to destroy the BT System themselves. However, their powers are not enough. So, in a last attempt, Drago lifts the BT System from the ground and lifts it up to the atmosphere. Just as the BT System detonates, Drago hears Wavern's voice telling him to not give up and that he cannot die yet. Drago, given new determination, absorbs the attribute energies from the BT System and evolves while easily destroying the BT System. He returns to New Vestroia, greeted happily by everyone excluding Spectra and Helios. Mira questions Spectra on their terms of partnership, but Spectra declares he works alone. Spectra returns to his ship and leaves, but not before Helios declares his continuing rivalry with Drago.

With the BT System destroyed and New Vestroia safe once more, the Bakugan are all moved back to New Vestroia from Marucho's house. The Bakugan thank the Resistance as they depart for Marucho's house while Klaus remains on Vestal in case the Vexos reveal themselves. Baron, Mira and Ace decided to stay on Earth to train and head to Dan's house for dinner. However, Marucho calls them saying that a strange ghost data has appeared in Bakugan Interspace in the form of unknown Bakugan, which is later known to be digital clones of Neathian Bakugan. Everyone heads into Bakugan Interspace and meet four Bakugan that even Drago doesn't recognize! The Bakugan do not communicate, so Baron suggests battling with them. Marucho creates a digital copy of Baron so his challenger, Haos Aranaut, has a partner brawler. The battle does not go so well for Baron, and things get even worse when Aranaut uses Battlegear, the same thing which Helios had! Aranaut defeats Baron and Nemus and destroys the field of Bakugan Interspace. Everyone begins suspecting that Spectra may have sent the phantom data.

While wondering where the Bakugan from Bakugan Interspace came from, Mira has just about given up hope on waiting for Spectra. Then, Spectra and Helios telepathically contact Dan and Drago to challenge them to one final match to prove they are the best Bakugan team. Drago uses his new powers to locate Spectra and teleport them to his location. The match begins and Drago appears to have the upper hand, that is until Helios whips out his Twin Destructor Battle Gear, which gives Drago a hard time. In their final fight, Drago calls on the power of his friends and defeats Helios. Spectra and Helios admit defeat and admit that Dan and Drago are the best brawlers. Drago didn't care about being number 1. Spectra decides to take off his mask and "work with the best rather than against him." Spectra becomes Keith again and Mira hugs him out of joy, happy to have her brother back.

Keith has easily settled in as the newest member of the Resistance, with the exception of a jealous Ace. Due to failure, King Zenoheld abuses his son then Mylene tries to stand up for him. However, King Zenoheld rejects her until Hydron places the blame on Professor Clay. King Zenoheld agrees to pit the blame on Mira's dad. Professor Clay discovers the secrets of the DNA code as well as where the transmission originated from (from Neathia). Meanwhile, Marucho analyzes the same data, as well as the one Keith received anonymously and discovers they are identical. Keith then suggests to construct Battle Gear for Drago. Drago denies at first, feeling it would be wrong being part machine but Keith assures him that the Battle Gear will be constructed from Drago's own DNA. This along with the lasting Vexos threat, Drago agrees, but must undergo a battle to test the virtual prototype. They enter Bakugan Interspace and Keith volunteers to use Ventus Hawktor and Subterra Coredem to battle Dan and Drago as Spectra! When Dan equips the gear, Drago struggles with it as his body is rejecting the Battle Gear. However, Drago continues to push forward and wins the battle, but nearly passes out due to the amount of power needed to control JetKor. Fortunately, enough data was gathered to construct Battle Gear that would not harm Drago's body. Shun and the other brawlers hope that Keith finishes Drago's battle gear before King Zenoheld and the Vexos do. The episode ends with Professor Clay telling King Zenoheld he has begin making the ultimate weapon against the brawlers and King Zenoheld agrees with his research.

Keith, Marucho and Mira work on constructing Drago's Battle Gear. However, Keith notices that Mira is distracted. Mira admits that she wishes their father would come around like Keith did so they could be a family. Keith doubts he will but offers Mira Gus' robotic bee to contact him. She does so and asks him to change sides, but Dr. Clay angrily refuses. Meanwhile, King Zenoheld changes his plan to destroy any living thing that stands in his way. Volt finds this plan goes too far and leaves the Vexos to return home while Mylene wishes him luck. However, his home is no longer what it used to be. Volt meets some children who still see him as their hero despite the things he did as a member of the Vexos and even promises to teach them how to brawl. As the children leave, Prince Hydron appears and a battle quickly follows and Volt easily takes the victory. Hydron is furious and throws a grenade that opens a dimensional hole beneath Volt, sending him into a far dimension (possibly the Doom Dimension). As Volt sinks into the portal, he vows that Hydron will get what's coming to him for all the suffering he has caused innocent people. While JetKor has successfully been completed, King Zenoheld is glad to hear that Volt has been taken care of, he warns the others that they will suffer the same fate if they cross him.

While the Resistance celebrate the success with Drago's Battle Gear, the Vexos begin to finish their plans for planetary domination. Lync remembers how nice Alice was to him and worries that she may be one of the casualties, so he copies the data for the Alternative System and heads to Moscow to give it to Alice. At first he hesitates, fearing that she may still be mad at him, but before he can make another move, Hydron appears and vows to destroy Lync. During the battle, Hydron implies that he wishes to leave the Vexos as well since he is mad that Lync has a choice to leave whereas he does not. Despite putting up a good fight, Lync is defeated and suffers the same fate as Volt. Before being completely dragged into the warp hole, Lync throws his glove with the chip inside in hopes that Alice will find it. After finishing cooking, Alice heads to find her grandfather and sees the results of Lync's battle with Hydron as well and finds his glove with the memory card. Alice gives the chip to her grandfather who insists they must show it to Dan and the others. When Keith asks how Alice found, she replied that Lync must have left it for her, but sadly adds that he may not be alive. Though the data suggests the Vexos Alternative System is incomplete, Keith states they will require the Bakugan DNA and Battle Gear data that they currently have, making them target for the Vexos once more.

King Zenoheld sends Mylene and Shadow Prove to collect the Brawlers' Battle Gear and Bakugan DNA Data so with the data the Alternative could be finished faster. Having followed Billy to Marucho's house in episode 37, Mylene and Shadow have prior knowledge to their hiding place. Once they arrive, they are ambushed by the Resistance, but Mylene takes Mira hostage! Keith quickly agrees to give them the data in exchange for Mira but instead he leads them to Bakugan Interspace. Despite Mira's attempts to change Mylene and Shadow's mind, a battle quickly follows between the four. Shadow is quickly and effortlessly defeated by Keith and MAC Spyder is destroyed in the process. Mira soon defeats Mylene and destroys Macubass. Keith offers Myelene a place in the Resistance but she bitterly rejects and throws one of Hydron's grenades. However, it results in a portal opening in Bakugan Interspace causing it to collapse, which means if it continues further causing the Interspace to shut down with the four of them still inside, they could be trapped there forever!

With Bakugan Interspace beginning to collapse on itself, Mira and Keith attempt to save Mylene and Shadow, despite her wishes to die rather than face dishonorment. Before she can change her mind, she and Shadow fall into the Death Ball's portal while Mira and Keith are extracted from Bakugan Interspace safely. Meanwhile, King Zenoheld learns of Mylene and Shadow's fall and blames their lose, as well as the Resistance obtaining the Alternative data, on his son Prince Hydron who he has tortured as a result. Later that night, Hydron has a dream in which Volt and Lync appear to him and tell him to take down his father and take the throne for himself. Though frightened by the dream, it motivates him to fight against his father. Meanwhile, Zenoheld's bakugan Farbros has been repaired and synchronized with the Alternative System. Hearing this, Hydron challenges his father and Prof. Clay transports them to the arena. Though Hydron quickly gains the upper hand, he is no match for Zenoheld's Assail Farbos. He loses and Zenoheld admits that they were never meant to be father and son and has Hydron imprisoned. While in his cell, Volt and Lync reappear telling him to overthrow Zenoheld. Hydron shouts he will defeat his father, while Gus Grav, presumed to have been killed in episode 39, listens from another cell.

Hydron discovers that a fellow prisoner is none other than Gus Grav, who was presumed dead in episode 39. Meanwhile, Runo, Julie and Mira prepare a cake for Keith to officially celebrate his joining the Resistance. However, Keith's mind lingers elsewhere, something that Mira notices but Keith brushes off. Dan suggests that instead of waiting for Zenoheld's attack, they storm the palace. Keith, however, is too impatient and takes his ship to the Vest Palace on his own. A battle quickly ensues and Gus feels Spectra needs his help, so he tricks Hydron into battling so their bakugan can free them from their cells and Gus leaves to help Spectra while Hydron is left on his own. When Zenoheld nearly defeats Spectra, Gus arrives in the nick of time, shocking Spectra who is happy finding out that Gus had survived. The two then battle together, giving them the upper hand against Zenoheld. Partway through the battle, Prof. Clay informs Zenoheld that the Alternative System, a giant airship modeled after Farbros, is complete and targets Spectra and Helios for a test fire. The blast sends Spectra's ship flying and takes a huge chunk out of a small planetoid, with Spectra and Gus just barely escaping the impact. Farbros links with the Alternative System and King Zenoheld declares his quest for intergalactic domination to begin.

With Keith having gone to the palace and having no way to find said palace, the Resistance are stuck. Luckily Alice and Dr. Michael arrive and use the teleportation signature left behind by Shadow and Mylene to back track to the palace. Meanwhile, Zenoheld continues his attack, forcing Spectra and Gus to retreat and come up with a plan of counter attack. The Resistance are saddened to hear that Tigrerra and Gorem do not wish to participate on the assault of the palace due to the fact that they know their limitations (which are lower than the rest of the team) and it would irresponsibly put Runo and Julie in danger. All of a sudden, Dr. Michael locks onto the palace's coordinates and the Resistance - minus Runo, Julie and Alice - head for the battle and arrive just in time to see Helios and Vulcan in trouble. However, the Alternative is far more powerful than any of them could have ever imagined (because despite the amount of damage they did, which was a pretty decent amount, the Alternative still repaired itself with Farbros). Keith realizes that because Prof. Clay built the Alternative, that he must be inside and asks Mira if she wants to confront him, which she does. Then, Keith uses a new battle gear, the Zukanator, on Helios, in hopes that it will even out the playing field. Keith blows a hole in the Alternative and he and Mira enter the machine.

With the battle against the Alternative pressing on, Hydron shows up to lend a hand. Meanwhile, Prof. Clay receives a video transmisson from a faraway world just as Mira and Keith arrive to make one final appeal. Once the brawlers realize Mira and Keith are missing, they deduce that the siblings may have found a way inside, so Dan uses Jetkor to blast a hole in the Alternative while Gus and Marucho stay behind to guard the rear. Gus and Vulcan are nearly beaten when Hydron steps in and saves him. Shun, having suggested to find the Power Reactor of the Alternative AND having memorized the blueprints of the machine, leads the Resistance through the Alternative. However, they are all quickly caught in a trap against four mysterious bakugan, unrecognized by Drago. While Mira pleads with her father to abandon his evil plans with Zenoheld, Dan and the others destroy the four unknown Bakugan as well as the Power Reactor. As they make their escape, Prof. Clay saves Mira from falling debris, but is trapped on the ship and Hydron captures his father, forcing them both to "go down with the ship." Prof. Clay returns to this computer and finds that the video he received depicts Bakugan in war. The Resistance go their separate ways as Keith and Gus thank Dan for showing them the error of their ways. 3 weeks later, Marucho has completely repaired Bakugan Interspace and uses Akwimos to test it while Shun uses Hawktor and Dan sticks with Drago. Then, they are approached by a boy named Ren who asks them if they're the Brawlers.

It's an all new adventure for the Bakugan Battle Brawlers when Dan's family moves to Bayview City and Marucho's Bakugan Interspace becomes fully operational to everyone, allowing kids all over the world to log on and display their battling skills. Dan heads to a cafe in town where Julie works to meet with his new friend Jake, a young brawler who is new to the game. The two make there way to Bakugan Interspace where they meet up with Marucho who gives Jake Subterra Coredem. Dan and Jake immediately want to battle, but discover that all the available arenas are occupied. They eventually meet up with Ren and Shun, who is locked in battle with Shuji. With Shun quickly seizing victory, Ren is scheduled to battle Dan next. As the battle intensifies, Marucho is forced to shut down Bakugan Interspace and Dan is knocked out cold. Before coming to, Dan has a vision of Bakugan at war each other, something which everyone, except Ren, brushes off as a hallucination.

On the distant planet Gundalia, the Twelve Orders discuss the explosion caused by Ren and Dan's battle in Bakugan Interspace. Kazarina, the head of the Bakugan Biology Research lab, is unable to identify the strong powerful Bakugan that caused the explosion. So, Emperor Barodius orders that this bakugan be brought to them before it joins their enemy. Back on Earth, Jake and Julie still believe that what Dan saw was a dream, though he is still convinced that it was real. Just then, Marucho calls and everyone heads to Bakugan Interspace, where Ren confesses that he is a humanoid alien being from Gundalia looking for strong battlers to help fend of the invading Neathians. Though hesitant, the Brawlers accept and track down two moles identified by Ren, Sid Arcale and Lena Isis and a battle ensues. Though Sid and Lena gain the upperhand, Dan pulls through with Jetkor and wins the battle. Everyone congratulates Dan on the victory. However, there may be more to Ren than meets the eye.

As Ren identifies three more Neathian moles (Mason Brown, Jesse Glenn, and Zenet Surrow), Princess Fabia from Neathia arrives in Bakugan Interspace looking for the recipients of the message she sent. Dan, having slept in, rushes to Bakugan Interspace and runs into Fabia, literally. Fabia learns that he is the top brawler in Bakugan Interspace, but before she can ask about her message, Dan rushes off to meet his friends. He tells them about the girl and Ren suspects she may be a Neathian spy. Before they can track her, Fabia arrives and is shocked to find that Ren, a Gundalian has gained their trust first! Now that Dan has sided with the Gundalians, Fabia claims they are her enemy and a battle ensues between her and Dan. Dan quickly takes the lead but falters when Fabia summons Haos Aranaut, the original Aranaut from which the clone Aranaut, Coredom, Hawktor and Akwimos originated, meaning Fabia sent the Phantom Data. This also means that it came from their enemies, the Neathians, something that Shun is not so sure of anymore. Defeated, Fabia leaves and wonders what to do now that Dan has sided with the Gundalians. While the others congratulate Dan on his victory, Shun disappears to ask Fabia what her side of the story is.

Dan gives Jake a practice match, but Jake feels he is not ready to become an official Bakugan Battle Brawler. When another mole, Mason Brown, is located, Dan challenges him to a battle, but Jake steps in and wants to prove himself. Due to his inexperience, Jake quickly loses and feels he has failed Dan in proving himself. The next day, Jake is still upset over his loss, so Julie, being a Subterra master, offers to help him discover his own battling style. Jake returns for a rematch with Mason while being greeted by a bitter crowd. With his newfound confidence, Jake easily defeats Mason. Before the Brawlers can pursue Mason, he teleports out of the stadium. Dan congratulates Jake, who becomes an official Battle Brawler.

With the Neathian moles making themselves known, they begin kidnapping brawlers from Bakugan Interspace. The puzzling part is that each brawler is eventually returned to BI. Meanwhile, Sid and Zenet find their recruiting hard when Marucho puts out an announcement to everyone not to battle Sid, Lena, Mason, Jesse and Zenet. In retaliation, Sid and Zenet challenge Dan and Ren to a battle. Ren is quickly taken out, leaving Dan to fend for himself. Being outnumbered, Dan loses but Sid allows him to keep Drago. After the battle, Gill of the Twelve Orders orders Sid to not engage the brawlers and to leave it to Ren, who states their plan is working perfectly.

Fabia tells Shun her side of the story, which he believes while he worries that the others have made a big mistake. While Marucho and Ren work hard on an expansion for Bakugan Interspace Jesse Glenn arrives. Dan heads to the new arena to challenge him but is stopped by Fabia, who claims that Jesse is not who he claims to be. Fabia steps in to fight Jesse, something that greatly confuses Dan and the others since they all think that both Jessie and Fabia are Neathians. Ren insists that they do not cheer for either of them and they should just let their enemies destroy each other. Despite this, Dan, Jake and Marucho cheer for Fabia. Although she puts up a good fight, Fabia loses due to a bug in the field, causing her to cry over her loss. Shun explains that the only person who could plant an unlikely bug that caused Fabia's defeat was someone familiar with the BI System, someone like Ren. Ren denies everything while Jesse flees. Fabia and Shun expose Ren for lying about how Neathia attacked Gundalia, causing him to run away. Marucho, however, refuses to believe these accusations and rushed off to find Ren.

Marucho frantically searches Bakugan Interspace and his home for Ren, but comes up with nothing. Meanwhile, Ren meets up with Sid, Lena, Mason, Jesse and Zenet, scolding Jesse for giving away his cover. Marucho uses a secret message to get Ren to meet him and they battle. Meanwhile, Fabia tells everyone her side of the story. Neathia was attacked by Gundalia and, due to their bakugan's inexperience in battle, they quickly lost to the Gundalian Bakugan. Fabia then sent out a distress message via the Phantom Data which lead her to BI on Earth. Shun discovers the battle going on between Marucho and Ren. When they arrive, Marucho defeats Ren. Ren attempts to get Marucho to switch sides, but he refuses to leave his friends. Ren declares their friendship over and reveals his true Gundalian form and tells Marucho that the next time they meet, they will be enemies.

After the battle with Ren, Marucho is refreshed and even constructs a speech program for the clone Akwimos. Fabia worries that Dan and the others do not fully trust her as they were easily tricked by Ren. Dan assures her that they completely trust her after seeing how angry she got about Bakugan being used for war. Relieved, Fabia gives Shun, Marucho and Jake the real Hawktor, Akwimos and Coredem. Meanwhile, Ren leads the other Gundalians to kidnapped two brawlers named Taylor and Casey. The two are taken back to Gundalia where they are brainwashed into fighting against the Neathians. Dan and the others confront Ren who sends Taylor and Casey to attack them. Dan and Shun battle Mason and Taylor while Marucho and Jake battle Sid and Casey. Fabia, however, sneaks off in hopes for finding Ren to discover his plans. After winning their respective battles and freeing Taylor and Casey from the Gundalians' control, they are all forced out of BI. Ren reveals that he is now in sole control of BI.

Dan and the others have been forced out of Bakugan Interspace and Ren has taken control! However it seems that they were the only ones kicked out as other kids continue to log on, not knowing what is going on. To make things easier, Marucho, Shun and Fabia head over to Dan in Bayview City aboard his giant airship. Dan tries to enter Bakugan Interspace, but is rejected. He tries to tell the other kids about the danger, but none of them believe him. Marucho is unable to shut it down as Ren has complete control, so Jake tries brute force, which actually works. Marucho takes them to a remote access room so they can plan their next move. Fabia remembers that the Neathian Bakugan can body shift themselves into Interspace. Dan immediately wants to go, but Drago reminds him he does not have that same power. So Jake volunteers and brings Dan along using Coredem's power. Dan and Jake witness brainwashed kids take back more kids back to Gundalia. The same two brawlers who accused Dan of lying reappear, now brainwashed by Gundalia, and battle Dan and Jake. They easily secure victory as well as the opponent Bakugan. The two boys are released from Gundalian control and Dan and Jake take them out of Bakugan Interspace. Dan vows to rescue all the brainwashed children.

With Ren still under control of Bakugan Interspace, Marucho quickly comes up with a plan to regain his beloved creation. Emperor Barodius calls Ren and suspects Ren may betray them due to his desire to not battle with his former friends. Ren assures him of his loyalty while Linehalt attempts to get the truth from his friend. Ren reminds him of the story behind their loyalty to Barodius: there were many ancient Bakugan with Forbidden powers but they were sealed underground. Eventually their numbers dwindled to just Linehalt. Ren was the last descendant of the Protectors of the Dark Bakugan and was assigned to take care of Linehalt. Over the years, they bonded and dreamed of escaping their underground prison until Barodius recruited them to lead the invasion team to Earth. Meanwhile, Marucho and Fabia infiltrate Bakugan Interspace. Marucho tries to regain control while Fabia and an Avatar Marucho battle Lena and Zenet. The Avatar is quickly taken out as Ren discovers Marucho's invasion. Fabia is defeated and Zenet and Lena decided to take her back as a prisoner, something that will give them an edge against Neathia. However, Marucho arrives in time to get her out. Though their mission was unsuccessful, Marucho reveals he installed a back door to better access Bakugan Interspace without alerting Ren and his team.

The Gundalians are easily overpowering the Neathians thanks to the brainwashed brawlers Ren got from Bakugan Interspace. In a last desperate attempt, the Captain of the Neathian Guard sends a Castle Knight, Linus to Earth to give Fabia the Element, the very thing the Gundalians are trying to take from the Neathians. As security tightens for the brawlers, their attempt to bring kids out safely is getting more difficult. However, many of the kids believe Dan and the brawlers over their wanted announcement. After Shun returns from saving more kids, he runs into Linus who is looking for Fabia. Though reluctant to trust him at first, they are attacked by Ren and Jesse and a battle ensues. Linus' partner Neo displays incredible power but the battle eventually goes to Jesse, who takes Neo as his victory prize. Linus is taken back to the others after being injured during the battle. He tells Fabia that having lost Neo to the Gundalians, he has also lost the Element, leaving Neathia doomed.

Dan and the others devise a plan to regain Neo while Linus desperately struggles to rescue his friend. Far too injured from the previous episode, Dan urges Linus to rest and leave rescuing Neo to him. With the Gundalian's search for the Element comes up with nothing, Ren is given orders to bring Neo to Gundalia on suspicion that he holds the Element. Before Ren can carry out these orders, Sid barges in and takes Neo, deciding to get a little glory himself and challenges Dan. When Sid finally throws in Neo, Neo gives Drago the Element, causing him to evolve into Lumino Dragonoid. However, Neo's body disappears in the process. With Drago evolving once again, Dan easily takes a win. Meanwhile, Neo appears to Linus in his dream to bid his friend a final farewell, his mission now complete. Julie comes into the room to find Linus crying over the loss of his best friend. Ren and Sid are berated for having lost the Element so soon after getting it. Sid's Rubanoid is taken by Kazarina for experiments while Sid is disposed of. Ren pleads for another chance, which the Emperor grants but implores Ren not to "test" him anymore, this was Ren's final chance to prove himself to the Emperor.

With Drago receiving the Element from the now departed Neo, the Brawlers decide to head back to Neathia to help fight off the Gundalians. Before they can do so, Dan must say goodbye to Julie, who hastily borrows his bike to get to her cheerleading practice. Meanwhile, Ren sends Zenet to steal the Element back via trickery. So, she disguises herself as Julie and tries to take Drago. However, her plan is foiled when the real Julie shows up, throwing Dan and Drago into confusion! However, when he reveals he is leaving for Neathia to help fight, the real Julie expresses that she is ok with it and hopes they succeed, assuring Dan that she is the real Julie. Zenet is forced to reveal herself and battles Drago. She tries to trick Drago by transforming Contestir's appearance, but Drago overpowers her with his new Battle Gear Cross Buster. Zenet retreats and informs Ren that the Brawlers are heading to Neathia. Ren runs to them before they go, but arrives just as they leave with Julie cheering them on, commenting that they will meet soon again.

As the Brawlers arrive on Neathia, Fabia introduces them to her older sister, Queen Serena. She then takes the brawlers to see the Sacred Orb, the true target of Barodious' conquest. Shun asks her whether it was this or the Element Barodius was after to which she replies that the Element was merely a portion of the Sacred Orbs power and that the Sacred Orb is the real target. Meanwhile, Barodious scolds Ren, Lena, Zenet, Mason and Jesse for seriously failing their initial plan to gain the Brawlers' trust and violenty commands the Twelve Orders to attack Neathia. The Brawlers do their best to hold the Gundalians off while Dan and Drago fight Barodius and Dharak Colossus but they succeed in breaking through Neathia's second shield. While the fighting is going on, Captain Elright, who was captured in episode 11, escapes from one of Gundalian's Stabber Knights and joins the battle. Just before Drago and Dharak can engage in further combat, the Sacred Orb suddenly teleports all the Gundalians away. The Neathians celebrate their victory as Fabia, Dan, Jake, Marucho, and Shun are made Castle Knights, the highest honor on the planet Neathia.

With only one shield left defending Neathia, it looks like Gundalia may actually win this war. However, Marucho devises a plan to distract the oncoming Gundalian attack consisting of Airzel, Kazarina and Stoica, while a small unit consisting of Shun, Dan, Fabia and their Bakugan head to the second shield generator to restart it. Marucho and Jake act as the decoys while Fabia leads Dan and Shun to the generator. When the battle gets too intense, Marucho and Akwimos trap Strikeflier and Avoir in ice and escape, while Fabia, Dan and Shun get closer to the generator.

With only one shield left defending Neathia, it looks like Gundalia may actually win this war. However, Marucho devises a plan to distract the oncoming Gundalian attack consisting of Airzel, Kazarina and Stoica, while a small unit consisting of Shun, Dan, Fabia and their bakugan head to the second shield generator to restart it. Marucho and Jake act as the decoys while Fabia leads Dan and Shun to the generator. When the battle gets too intense, Marucho and Akwimos trap Strikeflier and Avoir in ice and escape, while Fabia, Dan and Shun get closer to the generator.

Shun successfully sneaks past the Gundalian guards into the second shield generator, but is ambushed by Lena and Kazarina. A battle quickly ensues and Lena is taken out and berated by Kazarina. When she and Lumagrowl begin giving Shun too much trouble, Dan and Hawktor suddenly arrive to save the day! Dan and Shun switch back their bakugan and Shun heads to the generator while Dan holds off Kazarina. Shun reactivates the shield as Drago powers it up with the Element. Realizing what is happening, Airzel, Stoica and Kazarina quickly flee before being trapped within the shield. As the brawlers celebrate their victory, all is not well on Gundalia. Kazarina knows she will be punished by Baridous for the failure, so she plans to use Lena as her scapegoat. Lena, however, is fully aware of this thanks to Gill, and attempts to get Phosphos to assassinate Kazarina before it can happen. Unfortunately for her, Kazarina is well prepared Phosphos is taken out by Lumagrowl while Kazarina disposes of Lena. Kazarina successfully blames Lena for the failure and speaks to Gill about how Lena somehow knew of her plan, suggesting that she knew Gill had tipped her off. Gill remarks that not everyone can be trusted in these hard times...while Ren overhears their conversation and silently apologizes to Lena for her fate.

While the brawlers help the Neathians rebuild, Jake has an argument with Dan, saying that they should keep pressing the attack on the Gundalians now that they have the advantage. When Dan and Marucho argue that they should help rebuild, Jake runs off into the forest, followed by Fabia. Meanwhile, Jesse fears that he will eventually suffer the same fate as Sid and Lena and escapes from his prison to Neathia. He is eventually approached by Ren, who has been sent to collect him. They eventually run into Jake and Fabia and a battle ensues, Jesse promising that he will return with Ren no matter how the battle concludes. Jake and Fabia defeat the Gundalians and Jesse willingly returns to Gundalia with Ren, having had one final battle. Kazarina and Stoica prepare to punish Jesse for his escape and lose to the brawlers while Ren attempts to spare Jesse by saying he was much a part of the battle as Jesse was. Kazarina, however, tells him that he can share that information with Barodius himself. Plitheon suddenly speaks out and begs to be separated from Jesse, declaring that he can't stand him, something that surprises Jesse. However, Lumagrowl and Lytherius attack Plitheon for turning on his master. Jesse forgives Plitheon, saying that co-stars often have friction between them, but Plitheon insists he means what he said, as he slowly fades away. Jesse remarks that the spotlight is on Ren now and is presumed killed, leaving behind the book he always carries. While Kazarina and Stoica are walking through the hall, Nurzak appears and tells them that although they can trick the others of their true intentions, he can see them for what they really are.

With the second shield functioning at an even more powerful rate than before, things are looking good for Neathia. Meanwhile, Nurzak and Kazarina are sent to do recon. Nurzak tells Sabator how Barodius' father, the previous Emperor, did not seek to attain the Sacred Orb, fearing that its power is too great, while Barodius is far too ambitious and down right stupid for engaging in such a quest. Mason, however, has plans of his own and escapes the ship, possibly to switch sides. Kazarina becomes infuriated because of what may happen to her, but Nurzak assures her that he and Ren will find Mason. While on their search, they run into Fabia and Marucho, who still feels bitter about Ren's betrayal. Marucho's emotions only become worse when Ren says that their entire friendship was just a ploy and that Marucho shouldn't let something so stupid affect him so. The battle becomes so intense that the Sacred Orb shoots out dimensional rays, that should one get caught in, they will be sent around the dimensions without any way back. Nurzak and Ren retreat while Aranaut and Akwimos attempt to shield Fabia and Marucho from the dimensional rays. Just before it hits them, the Sacred Orb stops but not before Mason and Avior fall victim to it. Back at the palace, Serena expresses how happy she is that Fabia and Marucho made it back all right, while everyone questions why the Sacred Orb acted so. Meanwhile, Marucho believes that Ren will return to their side. However, things don't look to good for Kazarina as she finally gets the punishment she deserves from Barodius, though she is kept alive. While in the hallway, she encounters Nurzak who tells her that he is leaving the Emperor and with Gill as the Emperor's right hand, she needs to find a place for herself quickly. He encourages her to join him, to which she agrees.

The brawlers decide to use the Sacred Orb to their advantage by convincing Gundalians who fear it's power to switch sides, namely Nurzak. Ren has a meeting with Barodius where the Emperor reveals that despite the failures of Ren's team, he keeps Ren around because of his potential. Later in the hallway, Linehalt asks Ren what is wrong, to which he replies the only reason they serve and obey the Emperor is because he was allowed out of the darkness he and Linehalt had lived in. Suddenly, Zenet comes in and begs Ren to help her, fearing that she will suffer the same fate as the others. Ren brushes her off and tells her she has nothing to worry about. However, she is not convinced. Contestir tries to cheer her up by agreeing with Ren, but Zenet tells him that Gundalians care nothing of loyalty and despite her morphing abilities she has no use to them. Then she overhears that Gill and Ren are leaving to Neathia to destroy the second shield again. She disguises herself as Ren to take his place in order to prove herself, but Krakix easily sees through the guise and Gill decides to give her a chance anyway. While Gill and Krakix gather data on the second shield to completely destroy it, Zenet must keep Shun and Hawktor off him. However, Shun proves to be too much for her to handle, so Gill steps in and nearly defeats Shun, that is until Dan and Drago arrive. Gill and Zenet are defeated and return to Gundalia, where Zenet greatly fears her punishment. However, Contestir convinces Gill that because he is Barodius' right hand man, he will likely have people plotting against him, and that he may have use for a spy and volunteers Zenet. Gill sees this as a good idea and sends her to spy on Kazarina as Nurzak. She pulls it off and returns with information that Kazarina and Nurzak and plotting to overthrow the Emperor. Despite a job well done, Gill and Krakix kill Zenet and Contestir. Zenet once again explains Contestir that Gundalians care nothing for loyalty. Contestir argues that he has always been loyal to Zenet. She begins crying and apologizes for not seeing it earlier.

Nurzak sends a message to the brawlers for a meeting to discuss a peace treaty. The brawlers are unsure but decide to take the risk anyway. Nurzak plans to use Kazarina's attack on the emperor as his chance to sneak away to Neathia and give the brawlers the Switch Code, something that can supposedly control the Sacred Orb. Meanwhile, Gill informs Barodius of Nurzak and Kazarin'a betrayal and heads to stop him before he leaves for Neathia. Kazarina arrives with her troops and reveals that she is actually working for Barodius as a triple agent! However, Barodius decides to deal with Nurzak via battle. When Sabotaur begins absorbing Dharak's power, it proves to be too much for him to handle. Barodius destroys Nuzak and Sabotaur and the entire building as well. The brawlers, still waiting for Nurzak, conclude that they have either been stood up or something has happened to Nurzak. Back on Gundalia, Barodius thanks Kazarina for her services while Gill vows to take Kazarina down, still not trusting her.

With one of the 12 Orders disposed of, Barodius secures the loyalty of the others or else they will face the same fate as Nurzak. 2-3 days are required before Dharak's Exokor is ready, so Dharak suggests that, in the meantime, they launch a smaller attack to distract the Neathians. Once again, the Gundalians rely on the kidnapped humans from Bakugan Interspace to do their fighting for them. Unfortunately for the brawlers, when most of the kids are beaten, the Gundalian brainwashing does not wear off. While Kazarina experiments on more bakugan, she sends Ren to collect more battlers from Bakugan Interspace while Gill sends Stoica with him. Stoica however, bails to do things his way leaving Ren on his own, while Linehalt suggest they rethink their loyalties to which Ren tells him they have come too far to switch sides. Meanwhile, the subterra brawler Fabia defeated in episode 3, Koji, attempts to get in to have a battle, but is stopped by Julie, who tells him about the Gundalian-Neathian war while Stoica watches from afar. Koji leaves, believing Julie's story is too farfetched, and Stoica convinces him to head to Gundalia where he and other kids are brainwashed by Kazarina. With more kids attacking, Dan and Fabia split off from the others and encounter a Bakugan Mobile Assault Vehicle, a highly evolved Battle Gear, named Implanton. Fabia immediately recognizes Koji but is unable to get him to remember her. Fabia decides to use an Assault Vehicle designed for Drago and has it uploaded to his Bakumeter, and while it is downloading, she holds off Koji. The upload is complete and Dan easily defeats Koji with the Drago's Assult Vehicle, but Koji is still under their influence. Dan vows to free all the kids from Gundalian control. Kazarina releases control and the kids are returned to Bakugan Interspace. Koji tells Julie about what happened and how he doesn't remember anything after meeting Stoica but he vaguely remembers Dan's voice.

Deep within Gundalia, Sid wakes up from statis and learns that he, Lena, Jesse and Zenet were not actually killed, but imprisoned. Barodius order the attack to commence at dawn while Kazarina continues with her experiments. Sid has managed to escape and notices Ren leaving with some troops. On Neathia, the brawlers stand watch, waiting for the Gundalian forces, which arrives at sunrise. Armed with a Bakugan Mobile Assault Vehicle, Drago quickly tears through the Gundalian forces. Drago is suddenly ambushed by Ren and Linehalt but the two are too evenly matched. Dan begins asking why Ren fights for Barodius to which Ren reveals Barodius gave him freedom. Dan mentions that the emperor put him in darkness and that Ren must have been happy being friends with Marucho, and even though it was a ruse, Dan knows he'd rather be fighting with them rather than against them. Ren shouts at Dan saying that he is Gundalian and he knows nothing, but Dan replies that he is also a Brawler. Dan tries to get Ren to join them, but Ren refuses to forget those who have fallen at his hands (Sid, Lena, Jesse and Zenet). The fight continues but Rubanoid suddenly enters, being commanded by Sid. The two press hard on Dan and Drago but Dan reveals another new Assault Vehicle, one which he can control and Dan easily wins the battle. Sid tells Ren that the others are still alive and Dharak attacks them. Sid knocks Ren out of the way and falls over a cliff, but not before giving Rubanoid to Ren to take care of and telling him to not worry about the others and to "do what he has to do." Dan begs Ren not to go, but he leaves without a word.

After his battle with Dan and Sid giving him Rubanoid, Ren is very confused as to what he should do. The invasion continues on as the brawlers continue to push back the Gundalians. Kazarina finishes her experiments on Dharak's Exokor while Ren visits Barodius. Ren asks why he has been spared while the others have been punished and assumes it has to do with Linehalt's "forbidden powers." Barodius promises Ren he will have everything he wants so long as he completes his missions. Kazarina informs the emperor of Exokor's completion and the 12 Orders clear a path to the second shield for him. The others hold off the rest of the 12 Orders but have trouble dealing with them. Meanwhile, Drago and Dan hammer on Colossus Dharak, but he proves to be far too powerful. Once again, Dan reaches out to Ren to get him to switch sides before continuing battling Barodius. Drago quickly falls to Dharak's immense power and the second shield is punctured. Barodius orders Ren to prove his loyalty by finishing off Dan and Drago. Linehalt asks if Ren is sure to which he replies he has no other choice. Dan tells Ren just to get it over with when Ren suddenly fires at Dharak and declares he is doing something he should have done a long time ago: fighting alongside his real friends.

Ren decideds he has had enough of Barodius' false promises and turns on him to fight by his true friends. Dharak however, chooses to let Exokor, Riptor, and Smashtor do the fighting, but eventually joins in a one on one battle against Linehalt. Meanwhile, one by one, the brawlers are taken out by the Twelve Orders (Although Shun managed to take out Kazarina before falling to Airzel). Ren takes a bad beating, so Dan decides to step in, but Linehalt and Ren ask him to stay out of the fight. Meanwhile, Queen Serena prays to the Sacred Orb to protect the brawlers from harm. Barodius begins taunting Ren, and Linehalt begins exhibiting his Forbidden Powers, to the points where they begin to tear Neathia apart. The Sacred Orb, in response to Linehalt's power, sends out its last defense: Dragonoid Colossus. Dragonoid Colossus arrives in time and subdues Linehalt before entering Dan's BakuMeter. Ren realizes that he must live in seclusion to avoid Linehalt's power from causing harm and begins to leave, but is stopped by the brawlers. They welcome him back into their group insisting that Linehalt's power could do a lot of good as it could harm, Ren, feeling happy to be accepted back to the group, transforms into his human form. Fabia, however, is not so sure about their new teammate.

With Ren back on the team, everyone heads back to Neathia, but discover that Ren has been left behind! Elright explains that, as a last resort, the third shield is programmed to expel anyone with Gundalian DNA. Dan asks if they can just shut the shield off to let Ren in, but Fabia refuses and leaves. Serena explains the origins of her hatred to the Gundalians: Aranaut was originally partnered with Commander Jin, but they were defeated by Kazarina. Jin was unfortunately lost in battle and Aranaut was taken captive and experimented on. Fabia single handedly infiltrated the Gundalian palace and rescued Aranaut. Serena then reveals that Jin was Fabia's fiance and that Aranaut has no memories prior to his rescue due to the experiments. While Marucho searches for Ren, Dan asks Fabia to give Ren a chance. So, everyone heads to to find Ren and Marucho as Fabia challenges Ren to a battle. The stakes: if Ren wins, he can stay, but if he loses, he must leave Neathia forever. Ren puts in Linehalt and Rubanoid but they both fall to Aranaut. Knowing the conditions of his defeat, Ren begins crying. However, Fabia is convinced that he has changed and welcomes him to the brawlers. Ren is made a Castle Knight by Queen Serena and swears loyalty to her and the brawlers.

Soon after Ren joined the Castle Knights, the Gundalians begin attacking the third shield. When they find that the third shield contains a DNA barrier, they retreat back to Gundalia for a new strategy. Meanwhile, the Neathians send out patrols to watch out for any Gundalians attacking while a geometric storm (something that disrupts their radars) is taking place, with the Brawlers divided into groups of two to help the patrols. Dan and Jake are in one group, and they soon find an Earth boy named Robin who claims to have escaped the Gundalians' clutches and wants to find his sister. Jake wants to help him, but Dan tries to hold him back, as it is too dangerous, fearing that it may be a trick by the Gundalians. Jake then decides to look for Robin himself, but it turns out to be a trap, as Robin was brainwashed by the Gundalians all along. Kazarina appears and challenges Jake to a battle. Jake doesn't back down and is determined to free the brainwashed children from the Gundalians. Meanwhile, Dan reports back what had happened and the others scolded him for letting Jake go out on his own, so they all go out to look for him. Kazarina lays it hard on Jake and proves to be to much for the inexperienced brawler to handle. Jake scolds Kazarina for using other people to do her dirty work, to which she replies all the children are safe back on Earth, having outgrown their usefulness as strong battlers and she now uses them to bring in stronger subjects...like Jake. The rest of the Brawlers arrive just as Jake is defeated. He apologizes for not having listened to Dan and is taken by Kazarina.

Jake has been captured by Kazarina and is tortured by her. Meanwhile, Dan eagerly wants to rescue him, feeling that their argument was his fault but everyone tries to talk him out of it. Just then Jake suddenly walks right back into Neathia, claiming to have escaped, however, Shun is not easily convinced of this. When Jake wakes up from his rest, Shun tests his theory by asking Jake if he remembers fighting to restart the second shield, however Jake remembers that he and Marucho were on decoy duty. Dan beings suspecting that something must be wrong with Jake when he begins suggesting making changes to the third shield. Later that night, Jake heads to tamper with the shield controller and get teleported to Dan, who had set the trap with Captain Elright earlier. Jake finally reveals he and Coredem have been brainwashed by Kazarina and a battle ensues. The battle proves to be too much for Dan to handle due to the new and powerful ability card Kazarina had entrusted Jake with. Just then, Shun steps in and they take out Coredem, however Jake does not return to normal and is taken back by Kazarina. Dan vows to rescue his friend.

Dan is still upset about losing Jake and wants to rescue him, but Queen Serena forbids it, as it is too dangerous. Frustrated, Dan recalls the day he first met Jake. Linus arrives to bring them all lunch, when Dan and Drago are suddenly pulled away by Dragnoid Colossus to a place between dimensions. There he meets Nurzak and Mason. Dragonoid Colossus explains that if Dan wants to leave, he must defeat him in battle and a battle ensues, Dragonoid Colossus easily gaining the upper hand. As the battle goes on, Nurzak explains that the Sacred Orb is the origin of all Bakugan and that Dragnoid Colossus has been tasked with protecting it. Only two are able to defeat him, the dragon of fire and of darkness: Dragonoid and Dharaknoid and if Drago loses, they will just be giving Dharak the chance to take the Sacred Orb. Dan and Drago manage to pull through and defeat Dragnoid Colossus. Dragonoid Colossus takes Dan and Drago and tells them the rest of the story of the Sacred Orb: the first two bakugan born from the Sacred Orb were Dragonoid and Dharaknoid and every bakugan was born from their DNA sequence. Drago accepts his responsibility and evolves into Blitz Drago. They return to Neathia, bringing along Nurzak and Mason, who decide to fight against Gundalia, although Fabia warns that she will be watching them. Riding Dragonoid Colossus, they head to Gundalia to rescue Jake.

While the Brawlers are on their way to Gundalia, Ren tells the others that he wishes to save the rest of his team from Kazarina's lab, to which the other Brawlers agree. Ren, Fabia, Mason, and Nurzak split off from the rest of the team to rescue them. Dan, Marucho and Shun make their way inside the palace to find Jake. Meanwhile, Barodiusorders Gill and Airzel to separate Dan from the others so that he may defeat Dan and take Dragonoid Colossus. Dan is separated from Shun and Marucho who battle Airzel and Gill. Shun manages to take out Airzel, but he and Marucho fall to Gill. Before Gill and Airzel can do anything else, Shun throws a smoke ball and the two of them escape. Meanwhile, Dan is still lost within the Gundalian castle when a door opens up to a strange room and he is confronted by Barodius.

Dan and Barodius immediately battle with Drago easily tearing through Dharak's Exokor. However, Dragonoid Colossus informs Dan that Drago and Dharak are too evenly matched and that Drago must win at all costs. Despite another evolution, it seems as though Drago barely matches up to Dharak in terms of power. Meanwhile, Nurzak suggests they split up again, himself with Fabia and Ren with Mason, in hopes of surprising Kazarina, having already lost the element of surprise earlier. Dragonoid Colossus explains that despite changing in appearance and gaining new powers, Drago has yet to reach his true evolution. Drago begins to worry that he is not worthy of protecting the Sacred Orb, but Dan assures him that they have defeated evil many times before because they believed in themselves. With Drago's confidence restored, a brand new ability is unlocked, which Drago uses to win the battle. Dan demands to have Jake returned and Barodius complies, but Jake is still under the influence of Gundalian hypnosis and attacks Dan, knocking him out in the process. Meanwhile, Nurzak and Fabia get close to Kazarina's lab where she and Stoica confront them.

Dan is caught off guard by Jake and is imprisoned in a cell that keeps Drago in ball form. Meanwhile, Fabia and Nurzak engage in battle with Kazarina and Stoica, giving Ren and Mason a chance to break in and rescue Zenet, Lena and Jesse. However, once they reach the lab, they are nowhere to be seen. Kazarina and Stoica press on the attack, causing Fabia and Nurzak to fall down a cliff. However that was part of their plan. Nurzak tells Fabia a story of a man who thrived to fight so much that he led a group of soldiers, including his daughter, into a battle they were unprepared for, resulting in the girl's death. Nurzak laments that Fabia reminds him of her. Suddenly, Kazarina and Stoica discover they have survived and another battle ensues. Meanwhile, Shun and Marucho have snuck into the palace under the guise of guards while Kazarina reveals a surprise: a hypnotized Lena, Jesse and Zenet. Stoica begins flooding the battlefield, forcing Kazarina, Lena, Zenet and Jesse to retreat. Nurzak saves Fabia while he and Sabator are carried away by the water. Nurzak has a vision of his daughter, Floria, and is pleased to know he will be with her soon. After Aranaut is unable to find them, Ren and Mason come across him and Fabia. Kazarina returns to where Dan and Drago are being held and tricks Dan and Drago into looking into her eyes. They fall, unconscious, and are put into a coma.

With Dan and Drago captured, Kazarina discovers similarities between Drago and Dharak's DNA and discovers a way to use that DNA to make Dharak evolve. Fabia informs Ren and Mason about Jesse, Lena, and Zenet being hypnotized so Mason takes them to Nurzak's secret lair. Meanwhile, Shun and Marucho split up to find Dan and Jake. Shun discovers Dan but is forced to escape after being discovered by Lumagrowl. Marucho however, gets dragged into a presentation in which Jake teaches the Gundalian soldiers how to defeat the brawlers. Marucho is so distraught by how much Jake has changed and challenges him to a battle. Marucho tries a number of times to reach out to Jake, but fails. After the battle is over, the floor begins cracking and Marucho falls. Luckily, Shun arrives in time to save him and they head to meet the others.

Ren and Fabia reunite with Shun and Marucho and regroup with Mason at Nurzak's secret lair. Meanwhile, Kazarina's experiments have succeeded and she is ready to splice Drago's DNA with Dharak's. This results in Dharak evolving into Phantom Dharak as well as his DNA no longer containing Gundalian DNA, allowing him to pass the third shield. In return, Barodius names Kazarina his second in command, demoting Gill in the process. Mason decides to go look for Nurzak, as there is a chance he survived while the others break into the castle to find Dan. As the Brawlers break into the Gundalian's lair, they run into all kinds of trouble. Ren has to stay back to face Gill, Marucho fights Airzel and Shun deals with Stoica. Kazarina prepares to finish Dan off and Jake is there to watch her, while Fabia is the only one left who will be able to find Dan in time. But Jake seems to be regaining control as he does not destroy Dan when given the chance to. Will he save Dan and snap out of his trance?

Just as Kazarina is about to finish Dan off, Jake breaks free of the hypnosis and stops her. Fabia arrives and holds off Lumagrowl while Jake and Coredem rescue Dan and Drago. During the battle, Kazarina and Lumagrowl reveal Aranaut's last time on Gundalia: when Jin was killed and he was captured. Aranaut reveals he knew the entire time and was only faking because Fabia had never mentioned Jin because she wanted to protect him. Dan comes too and he and Jake join the battle, causing Kazarina to run away. Dan, Jake and Fabia reunite with the others and fight the Twelve Orders. The Brawlers suddenly notice that Barodius is missing: he has gone to Neathia to attack!! Dharak destroys the third shield and the Gundalians lay waste to the city. Dragonoid Colossus appears to take everyone back to Neathia, but the Twelve Orders summon their bakugan to stop them.

The brawlers must head back to Neathia to defend it from Dharak's attack but Kazarina, Stoica, Gill and Airzel are determined to keep them on Gundalia. The brawlers manage to fight them off and escape, but Fabia remains behind to fight Kazarina, as she has a vendetta against her for the death of her fiance, Jin. The brawlers quickly make their way back to Neathia, with the Gundalian forces close behind, as Elright and Linus who has Rubanoid as his partner attempt to fight back. Meanwhile, Fabia and Aranaut are taking a beating and things look grim. Suddenly, Avoir flies in and saves them with Mason and Nurzak as the brawlers arrive on Neathia.

Just as the Brawlers return to Neathia, Fabia and Kazarina continue their battle. However, Lumagrowl begins disobeying Kazarina's orders and is determined to finish off Aranaut with or without her. . Nurzak confronts Kazarina and tries to convince her that Barodius is just using her but she refuses to listen, claiming that Barodius will make her his queen. She flees from the battle and is confronted by Gill, who kills her, thus freeing Lena, Zenet and Jesse from her control. Ren fills his ex-teammates on what has happened and Lena, Zenet and Jesse decide to join and fight for Neathia, changing back to their human forms. As Fabia, Mason and Nurzak make their way back to Neathia, the epic battle between the Brawlers and Phantom Dharak begins.

Nurzak, Mason and Fabia attempt to return to Neathia on Nurzak's ship but they are stopped by Gill, though they do manage to escape and arrive just in time to help the brawlers. Lena, Zenet and Jesse are surprised to see Nurzak and Maron alive, but are nonetheless happy. Gill arrives on the scene and tries to convince Barodius that Fabia killed Kazarina, however, Barodius knows it was Gill who killed her and shoots down his ship, along with Airzel who tried to save him. Barodius leaves to confront Queen Serena so Dragonoid Colossus takes Dan to the Palace to protect the Orb while the others hold off Dharak. In an show of outstanding power, Dharak shoots down Dragonoid Colossus (along with Stoica), who drops Dan at the Palace, and returns to lay waste to the rest of the brawlers, leaving him and Drago the last ones standing. Barodius confronts Serena, who refuses to back down. Barodius prepares to attack her, but Dan arrives in time to stop him. However, the Sacred Orb teleports them to an unknown area and reveals itself to be called "Code Eve."

Code Eve explains that in the beginning, Dragonoid and Dharaknoid had battled each other and the result split the universe in two (Dragonoid's half formed into Vestroia and Dharaknoid's half created Neathia and Gundalia) which is why she had brought them to a mid dimension to battle, so no innocents would come to harm. Drago struggles against Dharak, and is knocked out and reverts to a primal state, relying solely on instinct, but Dan manages to snap him out of it. Meanwhile, everyone awakens after being defeated by Dharak and Linehalt is upset at the devastation so he uses his Forbidden Power to restore the war torn Neathia. Drago eventually manages to defeat Dharak and they are all returned to Neathia. However, Barodius decides to take the Sacred Orb's power for himself but its power is too much for Dharak to take in and they are destroyed. Code Eve awards Drago the Sacred Orb's power and he evolves into Titanium Dragonoid. With the war finally over, Nurzak, Ren, and the rest of his team create a formal alliance with the Neathians leave to form a new government on Gundalia. Dan, Drago, Marucho, Shun, and Jake return to Earth, and say goodbye to the Neathians as well as Akwimos, Hawktor, and Coredem (who must stay on Neathia). The four Brawlers return to Earth and are greeted by Julie and Dan's mom. Later, they return to Bakugan Interspace, where everything has returned to normal and Dan ends up battling Koji.

It has been one year since the events in Gundalia, and Bakugan Interspace has grown greatly. Marucho has teamed up with a Bakugan from Gundalia, Tristar, while Shun's partner is Taylean, a Bakugan from Neathia. After winning a battle, Dan and Drago learn that there have been two groups of battlers, Team Sellon and Team Anubias who have risen to high ranks not far behind Dan. Dan has a nightmare the following night in which a mysterious entity demands that Dan give him something. Drago, who also had a vision of a bakugan during the earlier battle, speculates that the two events may be related. Unconcerned by this deadly and skilled competition, Dan challenges Ben, a member of Team Anubias to a brawl. While Dan and Drago initially struggle due to the battle environment and faced against two bakugan. They struggle and just before they are about to lose, the entity again appears to Dan (Drago sees the image of the bakugan) and tells him to release his hidden power and destroy ben and his bakugan, also giving him all the power. They ultimately pull out a win after realeasing that power. However, Drago is unable to control the power nearly destroying the arena. This leaves Dan and Drago to wonder about the dangers of this latest discovery and if they are a threat.

After Dan's battle with Ben, Marucho and Shun talk to Dan about having Drago sit out for a while. Dan, however, shrugs it off and says he'll get Drago's powers under control, but secretly, he's extremely nervous about the amount of power Drago unleashed, and the two of them decide to go train to get it under control. Meanwhile, Marucho decides to have a battle to make up for Dan having to sit out, so he fights against Jack of Team Anubias. He and Tristar struggle to win against Jack and his Guardian Bakugan, Aquos Krakenoid. Meanwhile, Dan and Drago locate an abandoned arena to use as a training ground, but shortly after, a mysterious Mechtogan that calls himself Zenthon appears and wreaks havoc on the arena. Dan and Drago try to defeat it, but it eventually flies away and reappears to interfere with Marucho and Jack's battle and devastating the arena. Anubias and Sellon team up to fight Zenthon but struggle to defeat it, not even managing to land a hit. Eventually, however, Zenthon flies off and Anubias and Sellon part ways. Marucho and Shun then speculate that, since Zenthon has the same destructive power as Drago, they may be connected. Meanwhile, the masked man, whose named is officially revealed to be Mag Mel, is trying to break free of his prison, but requires more energy from Dan and Drago to do so. One of his hooded servants (who looks a lot like Sellon) informs him of the Mechtogan attack. He is astounded that Drago has that sort of power and tries to absorb more energy from his Darkas Dragonoid (or possibly Dragon and Dan) and begins to break free.

After Dan refuses to sign a few autographs and say hello to his fans, Anubias challenges the "big shot" to a brawl and Dan accepts the challenge. Both win one round because Drago tries too hard to control his powers and didn't focus on the battle. Dan is afraid of another power overload, so he tells Drago to run and not to fight. Anubias uses the opportunity to strike Drago and wins the brawl. Upset by the loss, Noah, one of Dan's biggest fans who had stood up for him earlier, becomes one of Anubias' fans. After the brawl Anubias tells Dan that he is disappointed that Dan brawled like an amateur, but still saying that he has respect for him.

Shun and Marucho find Dan and Drago training secretly and they discover that the Mechtogan Zenthon originally came from Drago. The next day Sellon and Dan have a match, but Shun and Kris from Sellon's team battle alongside making it a tag-team battle. Drago has a lot of difficulties controlling his powers and almost releases Zenthon, but Shun prevents this from happening by syphoning off Drago's excess power. Dan and Shun manage to pull out a win, but Sellon throws the battle and wins over the audience. Shun confronts her as to why she let them win to which Sellon offers Shun to join her team which he declines.

Tension between the Brawlers rises when Shun suggests that Dan take a break from battling as to avoid another of Drago's power overloads. However, Dan interprets this as Shun not trusting him and they have a fight. Shun is later confronted by Sellon, who still wants him on her team, and suggests that he give Dan some tough love. Later, the Brawlers are challenged by two boys calling themselves the Tri-Twisters. Shun and Marucho decide to take it themselves without telling Dan but have trouble against the opponents. Dan discovers this and wants to help, but begins to realize that Shun may have had a point earlier. They then discover that there is a third Bakugan, previously attacking invisibly, present. Sellon and Anubias suddenly interrupt the battle, wanting to teach the boys a lesson in honor and easily defeat them.

Dan still refuses to listen to Shun and Marucho when they tell him to take a break from battling. Even though he is still plagued by nightmares about Mag Mel and Razenoid, Dan doesn't mind battling Anubias with the winner being crowned the official number one brawler of Bakugan Interspace. Shun and Marucho tell Dan that they still think he should not fight, but will support him anyway. Dan thanks them and promises to reveal everything after the battle. During the fight, a vision of Mag Mel and Razenoid appear and Dan and Drago think they are fighting them instead of Anubias, causing them to lay waste to the field and endanger the crowd. To make matters worse, Zenthon reappears and everyone learns that Drago created him. Once Zenthon leaves, Dan and Drago's vision are returned to normal. The battle is declared over and Dan is disqualified for illegally using Zenthon (even though it was unintentional) and Anubias is crowned number one of Bakugan Interspace. Unable to face his fans who have turned against him, let alone his friends, Dan packs up his things and leaves.

Dan and Drago have disappeared and all sorts of negative rumors are spreading throughout interspace. Team Anubias is dominating the battle field now that Anubias is number one in the rankings. Shun and Marucho arrive in Interspace and discover that brawlers are now using BakuNano, equipment much like Battle Gear that greatly strengthens and amplifies a Bakugan's abilities to innumerable uncontrollable power levels. When they question Dylan, they discover that the upgrade for the BakuNano just appeared out of nowhere. Sellon has another talk with Shun and suggests that he take the position of leader of the Brawlers and put an end to BakuNano use since Dan and Drago are gone. Their conversation is interrupted when Marucho is brutally defeated in battle by the Bash Brothers, two boys using BakuNanos. Shun arrives on the scene and battles the two brothers. He managed to defeat them despite not using any BakuNano himself. He speaks out to the crowd that as the new leader of the Brawlers, he will abolish the harsh and dangerous style of brawling accidently set off by Dan and Drago. Sellon is then seen stating that Shun has fallen right into her trap. The episode ends with Dan and Drago suddenly arriving at New Vestroia.

Dan and Drago arrive in New Vestroia to train in an attempt to control his new powers. In Drago's secret training area, Dan and Drago find Aquos Amazon, Preyas' student, and Preyas himself. Amazon, having heard all about Drago from Preyas, wishes to battle with Drago. However, Dan and Drago are unsure as they may lose control again. Dan determines that each time Drago has lost control it has been in Bakugan Interspace, a virtual world, and the result may be different in the real world. While Drago and Amazon begin battling, Mag Mel and Razenoid begin feelings Drago's immense power, deducing that he is battling in the real world. During the battle, Dan and Drago suddenly have another vision of Mag Mel and Razenoid and they pass out. Preyas and Amazon leave while Dan and Drago rest. Back in Bakugan Interspace, Shun is dominating the battle field and defeating opponent after opponent. Marucho is impressed but thinks that Shun should take it easy. Shun, however, brushes him off and declares that as the new leader of the Brawlers, its up to him to get the Brawlers back on top but Marucho wonders whether as a member of the Brawlers, he should have a say. Back on New Vestroia, Dan and Drago are worried that their visions have carried into the real world, while Mag Mel and Razenoid have found them in New Vestroia.

Mag Mel sends Anubias to New Vestroia to battle Dan and Drago and harness their power. Drago, however, wishes to train on his own and away from Dan. Just as Anubias arrives, he attacks Preyas and Drago with Dan and Amazon making their way to Drago. Preyas steps in to defend Drago, but Anubias summons his own Mechtogan. Preyas proves to be no match for the Mechtogan, putting Drago into a rage and causing him to summon Zenthon. Drago loses control of his powers and lays waste to the battlefield, but Dan manages to snap him out of it. Zenthon attacks Drago and Drago determines that they will have to tame Zenthon in order to control it, which they manage. However, Anubias continues to attack Drago, but Zenthon stops them and Dan and Drago defeat Anubias, causing him to flee. Preyas and Amazon vow to help Drago control his new powers.

Shun has been battling far more frequently since taking the position of leader of the Brawlers, and it's starting to take it's toll on him. However, he shows no signs of backing down when he enters a battle royale. Things get tough when up against Robin from Team Anubias and Soon from Team Sellon when Taylean suddenly spawns a Mechtogan, Silent Strike. Shun tries his best to defeat it and is rescued by Rafe and Paige. After Silent Strike flees, Rafe and Paige reveal that they are a Neathian and Gundalian, respectively. They have learned that the Mechtogans are the offspring of chaos when there is a lack of sync between a brawler and their Bakugan and Princess Fabia has sent them to help the Brawlers. Shun, however, refuses the help and leaves while Marucho's father asks him to quit the Brawlers.

Drago continues to struggle gaining control of Zenthon and worries that it is because he and Dan are out of sync so they continue training on New Vestroia. Paige and Rafe worry that the Brawlers are slipping and Marucho thinks about his father's offer to quit the Brawlers and fix Bakugan Interspace properly. Wavern suddenly reappears and speaks to Dan and Drago and tells them that they must reconnect with everyone, namely their fractured relationship with the Brawlers. Marucho takes his father's advice and quits battling and work in his family's company with his father, but Tristar convinces him otherwise. Marucho fights Jack of Team Anubias and wins, thanking Tristar for reminding him that friends stick together no matter how far apart they are. Marucho's father and Kato witness the battle and express their pride in Marucho. Dan and Drago finally get back in sync and Wavern encourages them to find out the truth behind their visions.

Wavern assists Drago and Dan in ridding them of their nightmarish visions while Bakugan Interspace holds a Capture the Flag style battle. Marucho attempts to dissuade Rafe and Paige in joining, but they declare that they have no reason to avoid battle. As expected, Shun joins the fight to try and control the chaos. Rafe and Paige struggle against Team Anubias, but Marucho arrives to assist them and Team Anubias is eventually defeated. Meanwhile, a weary Shun and Taylean encounter Team Sellon. Marucho and Trister arrive at the flag but Sellon intercepts them and defeats Marucho. Paige and Rafe arrive just as Sellon summons her Mechtogan, Braxion. Rafe and Wolfurio distract the Mechtogan allowing Paige and Boulderon to take the flag and win, all according Marucho's plan. Shun arrives and sees the success of Marucho's plan and believes that his solution may have been wrong. Dan and Drago see Mag Mel and Razenoid again, following which Dan realizes Code Eve is involved.

Shun refuses to listen to Marucho's reasoning so Marucho enters a tournament to battle Shun. Meanwhile Wavern suggests to Dan and Drago to go back to the memories to when they first met Code Eve and how Dan and Drago received their powers. After doing this Dan and Drago realize an important clue they missed when Code Eve gave them their powers. Back in Interspace, it's a fierce battle between Marucho and Shun but Shun wins. However, Shun has taken Marucho's words to heart and realized the error of his ways. He and Marucho patch things up and promise to work together now. At the end of the epsiode Mag Mel tells Anubias and Sellon on why Dan and Drago can't control their powers and assigns Sellon to travel to New Vestroia and capture Dan and Drago by any means necessary.

The Brawlers, now back together, are dominating as a group and face Team Anubias in the next round. Sellon arrives on New Vestroia and fights Dan and Drago. Although they put up a good fight, Drago is forced to summon Zenthon, who now fully obeys Drago without question. Things take a turn for the worse when Sellon suddenly summons three Mechtogan at once! Dan, Drago and Zenthon combine their power and end up summoning a Mechtogan Titan, which easily wipes out Sellon's Mechtogan. Sellon tells them they can keep their gate and key and that the end of the world is still coming before leaving. Back in Interspace, Chaos Bakugan are suddenly released and are destroying Interspace, interrupting the battle between the Brawlers and Anubias.

With Bakugan Interspace under heavy attack from Chaos Bakugan, the Brawlers quickly jump into action. Anubias gives his team all his Bakugan before meeting up with Sellon to observe. The Brawlers make a plan to lure all the Chaos Bakugan into a single area and then delete it, despite the massive damage it could cause to the system. The plan is successful, but Marucho is halted by a lingering Team Anubias. All of a sudden, a mystery figure enters and when the dust parts, it is none other than Spectra! Spectra easily wipes out all the Chaos Bakugan with Darkus Infinity Helios when all of a sudden Team Anubias and Team Sellon's Bakugan attack them, followed by another wave of Chaos Bakugan. Dan suddenly arrives, having felt the distress in New Vestroia, with Drago to help.

Dan arrives back in Interspace much to everyone's shock and attempts to use Zenthon to shows the others that he and Drago are finally in control of their powers. While at first Drago and Zenthon are battling well, the latter is suddenly no longer under Dan's control and Mag Mel receives a massive flux of power. Anubias and Sellon retreat as the Brawlers leave the section of the Interspace which is then deleted by Marucho. Before departing, Spectra informs Dan that he has changed greatly and that the Brawlers aren't the team they used to be. The rest of the Brawlers mercilessly pile on Dan for leaving them to fend for themselves. Suddenly, Mag Mel and Razenoid break free and Mag Mel assembles a massive force of Bakugan. Later that night after being frustrated by his friends' hurtful words, Dan sees a vision of Gundalia being attacked by Chaos Bakugan! Marucho, Shun, Rafe and Paige prepare to head out to help Gundalia with the intention of leaving Dan behind due to the danger he represents. However, Dan insists on coming stating that he is the original Battle Brawler and will not be cut out off this fight.

The Brawlers arrive on Gundalia and hook up with their old friend Ren, who has now risen through the ranks of the Gundalian Army. Fabia, now the Queen of Neathia, is preparing to send reinforcements. Dan has a vision of Mag Mel's troop movements and the Brawlers set up a trap. The Chaos Bakugan arrive and Rafe gives Dan Bakunano as the Brawlers begin to attack. Mag Mel and Razenoid arrive and Mag Mel reveals that while Dan has had vision of Mag Mel, Mag Mel has in turn been having visions about Dan. Dan and Drago summon Zenthon while Mag Mel counters with summoning his own. The power is too great and Dan loses. Mag Mel and the Chaos Bakugan retreat as the Castle Knights arrive and the Brawlers begin to look at Dan's link to Mag Mel as a liability to their security.

As the Brawlers mount another attack on the Chaos Bakugan, Dan is forced to sit the battle out due to the compromise of his psychic link with Mag Mel. Dan receives another vision and realizes that Mag Mel are only after him and Drago, so they set out to confront him. On the way, they are intercepted by Shun and Taylean, who try to stop Dan from proceeding. Suddenly, Anubias and Sellon arrive and attack with their Mechtogan. Shun is taken out and Dan fights back with the help of Zenthon and Zenthon Titan and Marucho suddenly appears to help. Though they win, Marucho berates Dan for disobeying his orders. Ren reports that Paige and Rafe are missing and have likely gone after Mag Mel. Dan, Shun and Marucho go after them but fall into a chasm.

Dan heads off to fight Mag Mel, one on one and learn more about this Gate and Key he keeps talking about. When he reaches the inner chambers of Mag Mel's fortress, Mag Mel reveals that the Gate and Key is a mutated version of the Switch Code that Code Eve gave to Dan and Drago. Anubias and Sellon appear as Mag Mel summons several Mechtogan. The other Brawlers arrive but prove to be no match for the Mechtogan. So, Dan and Drago share their powers with the others, allowing them to summon their own Mechtogan. Spectra also arrives on the Vestal Destroyer and the Chaos Bakugan and Mag Mel are defeated. Dan realizes his mistakes with his friends and once again become the leader of the battle brawlers. Despite their victory Razenoid was able to collect the Gate, meaning that Mag Mel only needs the Key from Dan to achieve his goal.

The Brawlers receive an urgent message from Bakugan Interspace and return there only to discover it in ruins and infested with Chaos Bakugan. They meet up with Team Anubias and learn that after they left for Gundalia, the Chaos Bakugan returned and destroyed most of Interspace, making it unable for people to log out. Chris and Soon arrive and Marucho discovers an old access point from which they can escape and Soon sends Sellon their coordinates. While they sneak off to the access point, Dylan reveals that he is just a package of data created by Interspace to grant the desire of Brawlers for more intense battles. Anubias and Sellon appear and reveal themselves, in their true forms as well as the fact that they were created by Mag Mel. This was a surprise of their teammates and the Brawlers. Rafe and Paige successfully take the other battlers to a safe spot and return to help Dan, Shun and Marucho. With Sellon and Anubias defeated, they return to the access point, only to discover that it has been damaged! Shun blames himself for causing it when all of a sudden, a rainfall not programmed into the system began to fall.

The Brawlers are trapped inside Bakugan Interspace and to make matters worse, Chris and Soon arrive with an injured Sellon, sure that she has changed her ways. Dan agrees to trust her, but Shun was suspicious thinking it was a trick. While the Brawlers fend off an attack, Sellon asks Dan to see her personally and when he did she attacked him and Drago and stole his Key. Shun arrives and chases her but is stopped by Chris and Soon's Bakugan, unaware that Sellon is still evil, allowing Sellon to escape. Sellon gives Mag Mel the Key, but he disintegrates and absorbed her declaring that her will to live would be better served as fuel for his Resurrection. The episode ends with Anubias jumping off a building preparing to battle Dan.

Anubias kidnaps Noah in order to get Dan to battle him in one last showdown. After being informed of this Dan arrives for the battle and Noah (freed after serving his purpose) and Shun observe the battle. Anubias tries many ways to gain the upperhand including using three Bakugan at once and later combining two of his own through mutation. He briefly gains an advantage due to the mutations but Dan regains control after summing Zenthon. As the battle reaches its climax, Mag Mel appears and takes Anubias' power, disintegrating him in the process. As Dan and Noah mourn Anubias' loss, Mag Mel is now much stronger and more powerful than ever.

The Brawlers agree that Dan should use his link with Mag Mel in order to escape. Meanwhile, Chris and Soon try to escape the Chaos Bakugan with the help of Team Anubias. Dan successfully uses his link to connect with Mag Mel and they battle. Soon, having lost the will to do anything since Sellon's abandonment, is useless in battle until Chris convinces her otherwise and they follow Shun into battle. Dan manages to smash Mag Mel's mask and sees the face of none other than Barodius! Mag Mel reveals that he once was Barodius and Razenoid was once Dharak but their contact with Code Eve caused them to be banished to another realm and encased in new forms as a prison. In the midst of the battle, Dan loses the link and reveals that Mag Mel is Barodius. Marucho manages to trick Dylan into helping him get a message to the outside world and contacts his father and Kato to help get them out.

Marucho reveals his plan to completely delete Bakugan Interspace while his father and Kato work on an escape plan. The Brawlers round up the remaining battlers in Interspace and prepare to leave Interspace when a hoard of Chaos Bakugan suddenly appear. The Brawlers remain behind as the others escape when a mysterious Mechtogan appears and takes out the Chaos Bakugan. Spectra and Helios arrive and give time for everyone else to escape, but are caught in the deletion process! When they arrive back on Earth, they discover a mysterious dark moon in the sky. On the other side of the portal, Razenoid has come out of his cocoon and evolved.

Dan and the others have arrived safely on Earth to find a mysterious dark moon in the sky and all the people missing, having been imprisoned in the dark reverse dimension of Earth. Mag Mel sends Mechtogan Titans of five different attributes to destroy the Earth's core and in the process, destroy Earth with the resulting explosion destroying New Vestroia, Vestal, Neathia and Gundalia in the process. Everyone splits up in order to take out the Titans when all of a sudden Spectra and Gus show appear to help, Spectra having somehow been able to escape Bakugan Interspace at the last minute. Despite defeating the Titans, another wave is suddenly dispatched by Mag Mel and Dan is agonized to see all of his friends taken down so easily. With help from Marucho and Tristar about the Gate and Key, Dan and Drago break free and lure Mag Mel and Razenoid to the dark dimension where they're final showdown will begin.

The final battle continues with Dan and Mag Mel, while the others are fighting the remaining Bakugan, Mechtogan, and Mechtogan Titans on Earth. Razenoid and Drago continue to fight and Drago is about to get hit, but Zenthon and Zenthon Titan come to protect Dan and Drago. Mag Mel and Razenoid then summon Dreadeon and Razen Titan (called Dreadeon Titan) and they continue to fight. Dan and Drago tell them that they should only be fighting them not the innocent but Mag Mel responds as it is an act of revenge and he doesn't care about nobility. On Earth, the drilling has gone to 70% and Spectra and Gus go attack. Shun summons Faser Titan to help while some fear there are too many. Marucho reassures them as Rafe and Paige continue to fight. Mag Mel begins to taunt Dan and he manages to get them to fall down. He tries to get Dreadeon and Razen Titan to kill them but Zenthon and Zenthon Titan defend them. However, the residual energy created from them caused an outburst of energy which not only destroys them but Razenoid absorbs it to become bigger and stronger. With the drilling up to 85%, the battling continues with more Titans being destroyed. Dan and Drago, however, are not doing as well as Mag Mel tells them about the energy collected from Bakugan Interspace. Noah sees a vision of Anubias inspiring him to fight on and telling him how much he grown. Chris and Soon then hear Sellon's voice and run towards it. Dan and Drago then receive power from the gate and key while Razenoid blasts Drago. When the smoke clears, Titanium Dragonoid isn't there and is replaced by Fusion Dragonoid! Razenoid then tries to aim at Drago but he constantly misses. He fires at Razenoid which manages to destroy him and breaking the gate and key of them. Mag Mel is about to die but not before saying that Dan is still doomed. Mag Mel then disappears. On Earth, all the Chaos Bakugan, Mechtogan, and Mechtogan Titans disappear along with the Dark Moon. Everyone else returned confused as shimmering dust falls from the sky. They then believe that Dan and Drago sacrificed themselves but then in a glowing light, Dan and Drago appear. Everybody is happy and ask him what happened with Dylan walking away with his signature lollipop. They asked how was the battle and Dan responds with it being easy.

After defeating the Mechtogan that appeared in Bakugan City, temporary peace arrives. The peace is not meant to last long though as a new danger known as Wiseman arrives. Armed with his Nonet Bakugan (evil Bakugan he has released from the Doom Dimension), Wiseman hopes to destroy all peace that exists between humans and Bakugan. Seeing no choice, the Brawlers and their new ally Reptak enter into battle with Wiseman, but once the battle begins, Reptak notices Wiseman's style is similar to his missing partner: Gunz. What could this connection be? Will this connection harm the universe?

Reptak struggles to get over the disappearance of Gunz while working with Dan and Drago, but everytime he sees Wiseman launch a Bakugan Reptak can't help but think of Gunz's launching style. Will Reptak turn against the team, or can Dan and Drago help him stay on the side of light against Wiseman and his evil Bakugan?

At the beginning of the episode it shows Shun and Jaakor training together. After they are done Shun takes off while Orbeum and Skytruss make an appearance and ask Jaakor to go with them to New Vestoria so that they could protect the Bakugan. Jaakor states that he needs time to meditate on this so they leave, Shun overhears the conversation and makes a decision to let Jaakor leave. Jaakor then has a talk with Shun and they decide to part ways so Jaakor could protect his family. Shun is soon confronted by Wiseman and his bakugan Spatterix and Stronk. The two Bakugan fight Shun and Shun is able to hold his own for a while until they gain the upperhand. Jaakor is about to leave until he has a feeling that Shun is in trouble. Jaakor aids Shun in battle and was able to take on Spatterix and Stronk. The two Bakugan fuse together to create Scorptak and their combined power was able to take down Jaakor and his students. Jaakor then has Orbeum and Skytruss to fuse with him and they become Magmafury, with their combined power they defeat Scorptak forcing Wiseman to leave. Wiseman remarks that he is learning more about the brawlers each time he fights them. Orbeum and Skytruss then go to New Vestroia to help protect the Bakugan there.

After Shun tells his story about what happened in his battle with Wiseman, the other Bakugan pressures Raidizen when he is going to be able to combine. Radizen has become upset because he is unable to have a combination, he is approached by Roxtor but ignores him. He is later taken by Marucho who tries to cheer him up to a water plant his family owns. The two of them are confronted by Wiseman and they battle against his Bakugan, Radizen is able to hold his own and beat the two that when mira enters with roxtor who had follow marucho on to the plane , but when they combine he has a hard time. Radizen then fuses with Roxtor because he jump and collide with and combine then the two are easily able to defeat them in battle at the end the bakugan are clean up while mira and marucho talks about the whole ordeal and radizen and roxtor still are fighting

Mira has been working very hard, using Vestal Technology to create some new Bakugan Battle Suits for Drago, Reptak, Radizen, and Jaakor but before they could test them out Mira collapsed of exhaustion due to her working so hard mean while julie wants to interview the brawlers and video time the whole seen mira is rushed to the hopisital. where she must stay for a week so kato ask if she needs any thing mira ask and kato leaves to run a favor. When Wiseman arrives trouble starts julie get a call that wisman is attacking they quickly act. the battle begins and he seems to have the advantage because the brawlers have one member short which was not good news for them and the bakugan bulid up enough power to summon the mechtagon knocking out dan. but luckily they hear Runo and she returns to help them out in the battle by sending the battle suits having known how they work and been inform how by mira and the plane dan shun and marucho active and easily win the fight dan tries to rip of the mask but fails. back at HQ everyone is happy to see her kato explains she is the favor kato had to get.

Wiseman reappears and attacks the amusement park that Bakugan helped create Bakugan Land. Julie decides to go and confront him as a reporter to see what his problem is, and the Battle Brawlers must try and find a way to contain the Nomads powers once again.