Durning a field trip at the Tokyo Tower, three girls from three different schools, are transported to a medieval like land named Cephiro. The girls introduces themselves, Hikaru, Umi and Fuu, who are all in the 8th grade, reguardless how they look. They are greeted by a wizard named Clef. Clef explains that their high ruler, Princess Emeraude was imprisoned by one of her guards name Zagat, high above the skies of Cephiro. He then explains that Princess Emeraude made it clear about the Legendary Magic Knights, who are destined to save their world.

Guided by Clef's words stuck in their head, they reach the Silent Forrest. They are dropped off by the big griffin like bird, and wonders how the hell are they getting into the mansion like place, when it's surrounded by a wall with no doors. Fuu suggests on knocking. Umi is very skeptical, but when Hikaru starts to knock on the wall, a door opens. They try to call for someone, but no one is greeting them. They have little arguments on not being rude, and decide to enter without permission. They do not know it, but a monster crawling in the ground, manages to get in while they walk in. The door shuts, and they enter the mansion. They wonder around a bit, until they hear noise coming from a room. It turns out to be a library, and they see mess coming from someone behind the chair. They ask if the person is Presea, but the person turns around. It turns out that the ""person"" is a cute Pikachu/Hello Jitty cross cover called Mokona.

While travelling to Eterna Lake, they run into a guy named Ferrio who saves them from a monster. Ferrio then offer them to be their guide to get out of the Silence forest. They say no, and try to lose him, but he still follow them. The girls then discuss about him being their guide, but they can't trust him, due to the fact he still a stranger. They let him be their guide and uses food as payment since they have no money. We then find out that Ferrio was an entertainer, and Princess Emeraude saved his life when they thought he stole in the castle. Princess Emeraude then told the guards that it was a gift (the egg looking treasure) to him. That's why he is on the quest to save Princess Emeraude. They then take rest (thanks to Mokona) in a huge room/tent. Hikaru wants to give Ferrio food, who is outside, but Fuu tells her she'll do it. The reason is, Hikaru is too kind, and might invite him in to stay with them.

The girls run into what seems like to be a deserted village. They are captured in a net, and find out that the villagers were hiding from monsters, corrupting their land. A monster then shows up, forcing the villagers to go back into hiding. They get the monster's attention by hitting it after going after a little girl. The monster attack them (setting them free), and with Hikaru's magic, she defeats it. Umi is happy, and suggests to hurry to Eterna to get Escudo, but suddenly falls to the ground. Hikaru runs to Umi, only to be challege by Alcyone, who was the one who injured Umi with her Ice Arrows. Alcyone is confident on beating them, but Hikaru's anger only makes her stronger. In the midst of fighting, Umi slowly wakes up, and sees Hikaru battling for her sake. Umi turns to Mokona and wishes for magic, where Clef's voice, proceeds to give her (since she is ready for it.) Umi stands up, and casts a ""Water Dragon"" spell that blasts Alcyone, who retreats. Umi once again falls d

Alcyone begs Zagato for another chance, to kill the Magic Knights, after saying she has a plan (this time). The girls reach a lake, thinking it's Eterna. Mokona tells them it's not Eterna. A monster then attacks them (it was the form of the lake) and Umi destroys it with her Water Dragon. The monster rain on them, making them glow, and they brush it off, after they dry up. They head for Eterna, as Alcyone watches afar, laughing to herself. They head on to Eterna, only to see a line. Mokona wanders off, and Hikaru follows. Hikaru tells Umi and Fuu to see this, and they are surprised to see that Eterna is two dimensional. To see the fountain, they would have to be high up. They want to get Escudo, so they jump into the fountain. The girls are then seperated, and put onto a test. Hikaru sees her pet dog named Hikari, Umi sees her parents, and Fuu sees herself. The girls are attacked by their test, and won't fight back. They then hear Princess Emeraude's voice, telling them abou

Ascot sends one of his worm creatures to kill the Magic Knights. Ascot decides to take a nap while his creature kills them. The girls gives Presea Escudo, along with their weapons. Presea proceeds to make them in another room, and the hear the monster. The girls tells Presea to take care of their weapons, while they handle the monster. The worm attacks the Magic Knights who are a bit sucessful in defending themselves, but it turns and heads for someone else... Presea! Weak, Presea finally completes their weapons, but the monster breaks into the room. The ceiling falls, and it hits Presea. The girls see Presea, and their new weapons (each of them have swords). They then use their new weapon to kill the monseter. They all rush to Presea who is at her last breath. She dies, and Hikaru sworns her revenge. Ascot wakes up from his nap and calls his creature only to find his remains killed by the Magic Knights. He swears he'll avenge his death as well.

Clef tells the girls with each earthquake that happens in Cephiro it means that Cephiro is falling. If Cephiro falls completely, they cannot go back to their world. He then tells then to become a Magic Knight, they would need to awaken their Machine. Mokona knows the way to each one. Ferrio, sees Ascot, planning an attack on the girls, and he tricks Ascot, by saying he would want to help. Ascot doesn't fall for it, and tells him if he could, bring the girls to him in the desert, where the monster would hopefully kill them. Ferrio meets the girls, and lure them into the desert. The monster attack them, but Ferrio finds out from Ascot, the monster can attack by sound. Using the orb (or the gift that Princess Emeraude gave, two, a set, a pair, etc.) Ferrio calls the monster and lure it away from the girls. A small monster then gives the message to the girls, saying that Ascot has taken Ferrio. If they want to save him, they need to go to the desert. They decide to sleep on it, think

Hikaru takes an estrange monster for caring. She names it Hikaru after her dog. We then find out that ""Hikari"" is actually a ""pet""/monster that Ascot was training. Hikaru spends too much time with Hikari and Fuu and Umi thinks she'd been hurt by a monster or something worse. They go out looking for her, and find a monster by Hikaru. They are ready to kill it, but Hikaru tells them it's Hikari. They don't fight it, but Hikari (or ""Bigot"" the real name) runs amuck on the forest, setting fires, etc. Hikari also knocks Fuu unconcious, and takes a hold Umi. Hikaru is mad, and kills Hikari. They bury Hikari, and experience an earthquake. They hurry off to find their Machines.

Alycone manages to trick Ascot into freeing her from a barrier that was holding her against her will. She promised him to give power to one of his monsters that would kill those Magic Knights. In an open field, Umi is still obessed with her fencing competition that would of been a week away when they originally arrived in Cephiro, even though weeks (or possibly a month) already has passed by. Hikaru suggest if you wish hard enough, maybe you can still make it at your competition, since Cephiro is a land of power. Both Hikaru and Fuu would pray for Umi too. A few yards away, Alcyone gives Ascot power to his monster named ""Luci"", which not only over powers it, but freezes itself, as well as Ascot as well. Hikaru, Umi and Fuu see the snow storm blasting their way, and Umi makes a wish before getting hit. She wants to return to Tokyo. Hikaru and Fuu suffer from hypothermia, and falls to the ground. Then Alcyone stops the weather and hopes that her plan on killing the Magic Knights work

The girls reach a lake, and Mokona reveals a Machine is in it. They travel underneath the water, to a place with air (thanks to Mokona.) Umi doesn't feel good, and starts to glow. She wanders off, and suddenly they notice a painting of a blue dragon. It's start to come out, and Umi is cut off from Hikaru and Fuu behind two large doors. Ascot then shows up with his monster, and battle the Hikaru and Fuu. They don't to much damage, but Fuu points out the glowing jewel on its head, and Hikaru breaks it. The monster becomes stun, and Ascot comes out. He then goes on how they all killed his monster friends. Hikaru tells him if they were his true friends, he would not hurt them or harm them in anyway. The monster wakes up, and starts to go berzerk on them. Ascot runs away, while Hikaru and Fuu fights it off. Meanwhile with Umi, the dragon tests her, by telling her to show her courage of the heart. She hear the screams of Hikaru and Fuu, and suddenly the doors disappear.

The girls are flying off to the flying mountain that the first saw when they were transported there. The mountain is holding the castle were Princess Emeraude is being held. When they almost got there, they were attacked by Zagato, but then saved by Princess Emeraude. Ferrio wass bored, and while resting, he brings out his comminucator. He then gets a message from Princess Emeraude to save the girls by the lake of Piraus Village. He does so, and they take rest there for a bit. Meanwhile, The villagers are being tortured by a servant of Zagato's named Caldina. When she demands money, she changes her mind, upon seeing the girls and Ferrio when they enter the village. The girls then tell the story on getting the Machine, and they are ready to save Cephiro. He then reveals that they need to acquire two more machines to complete their journey before they can save Cephiro.

The girls are travelling, when Mokona tells them to go up. Mokona then reveals a Machine is up there in one of the flying mountains. Caldina and Ascot manages to catch up with them. Caldina tells Ascot, she'll take care of everything, and tells him to wait for her. Caldina uses a spell to think the ground is soft and shaky, as well as big rocks falling on them. THe girls panic, and fall to the bottom. They wake up and see a cave, when the ground continues to shake. Once inside, they see Clef, where he tells them he had save Princess Emeraude, and she wants to talk to them. Fuu isn't convinced, and warns the others, saying it's too easy. They enter another room, where they see Princess Emeraude, and two guards with her. Fuu then questions how they could defeat Zagato. Princess Emeraude and her two guards then turn into monsters, and proceeds to attack them. Although they cannot hurt them, the monster can. Hikaru, Umi and Fuu knows it's only an illusion, and tries to concentrate

Caldina is determine to kill the girls inorder to receive the pile of money from Zagato. Ascot doesn't care for it anymore, and tries to convince Caldina not to attack them. Caldina uses her ""bells"" to hypnotize Hikaru and Umi against Fuu. Fuu uses her magic to hold back them, and doesn't know Caldina is only a few steps away. Caldina reveals herself, and forces Fuu to attack Hikaru and Umi. Ascot blocks an attack, and Caldina stops and freezes him. Fuu manages to break thru, and hits Caldina with a spell. A few moments after, Caldina and Fuu start to talk. Fuu explains, even though they don't know each other well enough, she cares for them. Fuu uses Ascot as an example, and Caldina sees the light. Caldina unfreezes Ascot, and Hikaru and Umi wake up. They want to attack her, but Fuu stops them. She sorta fill them in about Caldina. Caldina and Ascot then proclaim not going back to the castle (or Zagato if you see it that way) and run off.

After battling a fierce monster, the girls find out that Mokona is able to project the land of Cephiro. They soon find out that they need to head for the skies for the other Machine, as well as their location (where they are currently at.) Soon after a bright light showed up, kidnapping Umi and Fuu. A picture of Clef (projected by Mokona's jewel) shows up and tells how there are unusual monsters, and other unimportant stuff and some back story that could be just brushed off. Hikaru remembers the map, and Mokona projects it. She heads towards Umi and Fuu's way and manages to get cut along the way due to some thorns. Mokona catches up with her, and notices the blood. Soon after the light is after Hikaru, but Mokona pushes Hikaru out of the way and in he goes into the light, while Hikaru falls into a ravine sort-like place. Hikaru tries to climb up, falls down, and manages to get hit in the head by rocks. She slowly figure out of the light monster work, and remembers that

Innova asks Zagato to have his turn to try and kill the girls, and he agrees. In Cephiro's very first storm, the girls take refuge in a cave, near the sky shrine, where another Machine is being held. When Fuu starts to worry about Ferrio, she brings out her communicator, only to be called by him. He tells them, he's nearby, and want to take refuge with them. Just before entering the cave, Ferrio notices a girl lying on the ground, holding a herb. Fuu is excited when she sees Ferrio's silhouette, but is crushed when he sees him carrying a girl. The girl then wake up, and introduces herself as Selah. She starts to explain she leaves on the bottom of the mountain, and needed the herb she had to cure her brother's fever. They then all take rest, but Fuu can't sleep. When she is about to talk to Ferrio, Selah beats her to it. Ferrio offers her some soup, she not only says yes, but offers to put the herb in it. She then gives it to Ferrio to taste.

Zagato informs Princess Emeraude that he is using mind control to send one of the Princess' skilled swordsmen/royal guard to kill the girls. She begs Zagato to stop, but he doesn't listen. With the girls, they are traveling to the volcano-like shrine to revive Hikaru's machine, only to be attacked by a big flying bird. They try to fight it off with their swords, but it's no use. It then takes a hold of Umi and flies off. Fuu tries to give Umi her sword, but Umi's sword turns into water while Fuu grabbed it. Fuu only has one choice, and throws her own sword to Umi. Umi catches it, but is too heavy. She tries to hold onto it, but drops it instead. The bird continues to fly, and a guy kills the bird. Hikaru and Fuu catches Umi, and she comments how heavy Fuu's sword is. Fuu then holds it, and it's light as a feather. They then soon figure out that the swords, was made specially for each other. Anyone else who tries to use it (including each other) it won't let them. Umi then wan

Innova once again begs Zagato to return him to his true form. To his surprise Zagato does, and Innova, who transforms into a wild beast wolf-like creature goes after the girls. Meanwhile with Ferrio, memories slowly come back to him, and is it revealed that he is Princes Emeraude's younger brother. He then runs to the girls. The girls are really losing, and when all seem lost, Ferrio communicates thru the orb, and tells them that Innova's weak spot is the jewel on his head. Hikaru manages to hit the jewel on Beast-Innova's head, killing him. Ferrio finally reaches them, and sees the girls trimuph over Innova, and tells them to save Cephiro! With everyone gone, Alcyone, begs Zagato to kill the girls, but he just leaves her begging.

Alcyone spies on Zagato, as he talks with Emeraude. She notices again, he is not physically attacking her, but merely just verbally making trouble. She slolwy gets more of her doubts with the ""kidnapping"" of Princess Emeraude. Mokona leads the girls into a hot (asui!) volcano where the last Machine is being held for Hikaru. Umi and Fuu starts to get worried about Hiakru when she acts weird, and is disappears (like the others did.) When this is all happening, Zagato manages to also get to the Volcano when Hikaru just went in. He strips Umi and Fuu's powers, just intime when Hikaru gets back. Hikaru and Zagato talk for a bit, and he takes her power also. They talk for a bit, for a little more, and he fires a fireball towards Umi and Fuu.

The girls start to head towards the flying mountain in the sky, and remembers the good times, and bad times they had. They then get a message from Princess Emeraude, telling them to grant her wish and save Cepiro. They finally reach the place, only to find Zagato in his own Machine preventing them to come any further. They fight, they get injured, and when it looks like they don't win, they combine all of their powers, Red Lighting, Dragon Water, and Green Gale. They shoot it towards Zagato, where it kills him. In the final scene Princess Emeraude screams in horor as Zagato is killed off.

The girls head to the castle where a girl, looking like Princess Emeraude is waiting for them. After mentioning Zagato's name, she goes berzerk, and climbs into her own machine. She starts to attack them, and they fly out of there (the girls are in their machines.) Once outside, they start to get into a battle with the machine, and get the truth from Princess Emeraude, saying it's her. She then tells them, how her sorta love affair (falling for Zagato actually) was a big no-no for the pillar who watched over Cephiro, and imprisioned herself so that feelings wouldn't get in the way. It was too late for that, and she reveals inorder to save their land, and fulfill her wish, they would have to kill her! She then reveals no one from Cephiro or suicide couldn't kill her, so that's why she summonded them. After attacking them, the girls combine into one machine, kill and proceeds to kill her. The huge light appears, and we see Princess Emeraude and Zagato together.

Hikaru, Umi, and Fuu have been reunited with their families, but their hearts are still not at ease. The three promise to meet each other at Tokyo Tower, the place where they first met. Suddenly, with another mysterious flash of light, the three girls are whisked back to Cephiro, where Mokona and Clef await them.

Now that Cephiro has lost its Pillar, Princess Emeraude, it is under attack from three countries – Autozam, Chizeta, and Fahren! Clef doesn't want the girls to get involved in this new war, but Hikaru Umi, and Fuu agree to it on their own.

Ferio greets the three girls upon their return to the castle and explains that he is the younger brother of Princess Emeraude. The three girls are reunited with their old friends Caldina, Lafarga, and Ascot. They are introduced to Lantis, the younger brother of High Priest Zagato, who recently returned home from Autozam.

Late that night, Umi visits Clef, to apologize for originally not wanting to become a Magic Knight. Meanwhile, Fuu and Ferio were talking about Princess Emeraude and Hikaru awakes from a nightmare, and wanders sleeplessly around the castle. She finds Lantis comforting Mira. Suddenly, Autozam's battleship NSX appears above the Sephiro castle.

Hikaru and company head out to survey the NSX, but before them stands Alcyone! Hikaru, amidst the attacks from Alcyone, tries to convince her to fight along side them, but suddenly a change befalls Alcyone! She beings talking with an eerie voice that Hikaru has heard in her nightmares!

Hikaru, Umi, and Fuu ask Eagle why Autozam is invading Cephiro, when a giant metallic dragon appeared above them! It is Dome, the mobile fortress of Fahren, led by First Princess Aska, who wishes to become the Pillar of Cephiro. The girls follow Eagle's FTO which flew off to spy on Dome.

The deterioration of Cephiro gains peed, and the girls must find a new Pillar soon. When about the qualifications for someone to become the Pillar, Clef shows the girls Princess Emeraude's crown. He tells them that only the one worthy of becoming the Pillar can touch the crown.

Hikaru and Lantis embarked on a journey in search of a new Pillar. Before them is a desolate wasteland so different from what Cephiro once looked like. In addition, the monsters that roam the land have grown in power. Eagle attacks the traveling pair and captures Hikaru. Lantis tries to follow, but Alcyone stands in his way!

Umi and Fuu, sensing Hikaru is in danger, get into their Run Gods and fly off. Meanwhile. Hikaru awakens from her dream with Nova realizing that she is aboard the Battleship NSX. She is taken to Eagle, where Eagle explains why Autozam is invading Cephiro.

"" am Nova, the one that will kill Hikaru..."" Hikaru defends herself against Nova who ruthlessly attacks. Umi and Fuu arrive, but the three Rune-Gods are dragged into an alternative dimension created by Nova. Debonair appears to the three girls.

Hikaru returns to the castle, but with her sword broken, she cannot call for her Rune-God. Meanwhile, Clef's group captures Alcyone and interrogates her. Clef, feeling something more behind Alcyone's words, becomes even more concerned. Suddenly, Bravada – the mobile fortress of Chizeta – arrives at Cephiro carrying the two princesses Tarta and Tatra.

Umi and Fuu head out to investigate without Hikaru, and encounter the guardian spirits of Chizeta. Aska from Fahren reappears in the skies above Cephiro for a rematch. Aska tries to prevent the Djinn from taking the two Rune-gods...

Hikaru sits depressed, unable to help her two kidnapped friends. Seeing Hikaru so sad, Presea is determined to revive the broken sword. Nova appears in Hikau's heart and tells her that every hardship she has faced is all Emeraude's fault. Hikaru, attacked by Nova's words, slowly falls into the darkness within…

Nova skillfully confuses Hikaru her by distorting her memories of Umi and Fuu. Nova uses Hikaru's feelings towards Lantis to break Hikaru's determination. Hikaru's fears and doubts cause her to fall deeper into the darkness. Can Presea help her?

Umi, held captive by the mobile fortress Bravada, is forced into an outfit from Chizeta and then locked into a cage. The younger princess, Tarta, feels deep anger watching Umi, challenges Umi to a swordfight.

Fuu, held captive aboard the Dome of Fahren, is brought before Aska. Upon hearing that the Rune-God is alive, Aska begs Fuu for one of her own. Fuu gently declines, but Aska doesn't listen. Fuu suggests an archery match, saying that if Aska wins she can have her Rune-God, but if she wins, she must be returned to Cephiro.

Aska tries to keep Fuu aboard the Dome, but Ferio jumps into the scene and rescues her! However, Hikaru's battle with Nova seems to be all but lost. Can Presea's desperate pleas to Hikaru reach the Magic Knight's heart?

Hikaru has returned after reviving Rayearth's sword, but doesn't remember confessing her love to Lantis! Hikaru later bumps into him in the castle garden en route to see Clef. Meanwhile, aboard the bridge of Autozam's battleship NSX, Eagle commands for the launch of the Laguna Cannon to see how Cephiro will react. The attack on Cephiro castle has finally begun!

Eagle, in combination with Geo's GTO, manages to break the barrier and enter Cephiro Castle. Inside, Alcyone responds to Debonair's call and allows the dark lady and her monsters to enter the castle! Selece and Windam attempt to block the GTO. Meanwhile Lantis heads for the top floor to confront Debonair at the crown room.

Hikaru dreams of Cephiro from when it was peaceful. There, she sees the conversation between Lantis and Zagato, with princess Emeraude watching from behind the columns. Zagato asks Lantis about the Pillar system, and he answers...

Umi and Fuu continue fighting the monsters in the castle's residential quarters. Hikaru chases after Nova, who had threatened to kill Lantis. Nova finds him with Eagle, and promptly attacks! Meanwhile, Umi and Fuu are struggling against the monsters, but they realize that the black sphere is taking in the children's fear to create monsters…

Hikaru confesses her dreams concerning Nova and Debonair since she got back to Tokyo. Geo, worried by the loss of communication with Eagle, decides to attack. Just then, Aska's Dome reappears! Seeing that the Run-Gods are not out to battle, Aska thinks that Fuu has been defeated and calls giant Sang Yung to protect her!

Eagle escapes from his cell and searches the castle for a way into the crown room. Since Eagle has biological data on Lantis, the intruder searchers for him and his sword. Eagle finds Lantis interrogating Alcyone and the two confront each other. Lantis sets to attack when Hikaru suddenly jumps into the battle! Meanwhile, Clef's rig and Lantis' sword start to glimmer...

The crown starts to change shape as Hikaru and Eagle both safely enter the crown room. But which will become the new Pillar of Cephiro? Just then, Tarta and Tatra of Chizeta arrive aboard the Bravada. Umi leaves Ascot to protect the castle and heads out. Tarta and Tatra challenge her to a personal duel. They tell Umi that if she wins they will stop their invasion of Cephiro...

As Umi and Fuu are continuing to fight the invasion of monsters storming the castle they discover the source of the monster's power are the children's fears being taken in like a big black ominous cloud spreading. Worried he hasn't been able to contact Eagle Geo makes the decision to attack, just then Aska shows up, not seeing the Rune Gods around she assumes that they have been defeated and calls out Sang Yung to protect her.

Eagle having been captured breaks out and starts searching for Lantis with his bio info he can then access the crown room. Lantis continues to interrogate Alcyone when Eagle confronts Lantis then all of a sudden Hikaru jumps into the middle of it as well.

The Crown room allows but Hikaru and eagle to enter but who will be able to handle or touch the crown to determine the new Pillar?

During the fight with Regalia, Hikaru tries reaching out to Nova who disbelieves what everyone says about Debonair while the new allies help comfort people in the castle. Lantis is trapped inside the rogue Rune God...

Nova is now back in Hikaru's heart where she belongs. With her dying breath, Alcyone unveils Debonair's location: Cephiro's alternate realm. The Magic Knights and their Rune Gods are ready to end the struggle once and for all...