As part of the organization Mithril, Sergeant Souske Sagara, Melissa Mao and Kurz Weber receive a secret mission: guarding Kaname Chidori, a popular student from a Tokyo high school who has hidden military potential.

Sousuke is set on his mission to protect Kaname, and attacks anything vaguely resembling a threat to Kaname. This leads to funny situations and Sousuke has to explain Kaname why he is following her, blaming coincidence.

Sousuke gets oriented in his Garbage Duty and Kurtz gets to know the targets a little better. Meanwhile Tessa takes care of a research center in Russia. Sousuke's team encounter a mysterious man climbing to Kaname's balcony.

The airplane with Sousuke, Kaname and 400 of their classmates is hijacked and brought to a secluded location. Kaname is taken away from the plane, but what will Sousuke do to rescue her?

Sousuke comes to Kaname's rescue, and the rest of the rescue team arrives on the scene as well, but can they hold off the army and save the students? Can Sousuke get Kaname to safety?

As the rescue team has left, Sousuke, Kaname and Kurz try to figure out a way to get back to safety.

Sagara and Kaname barely escapes from the enemy. Now on the run they try to find a way out. Deep in the forest Sagara isn't able to move much more with his injuries, so Kaname decides to stop and rest for a bit. After Sagara was able to stop the bleeding, Kaname realizes how dangerous and mysterious Sagara really is. To make matters worse they find an unexpected person along the way, it's Kurtz, who looks badly beaten by Gaul. As the 3 try to make to the shoreline they find themselves in a tight pinch; the forest ended and all there is now is plain fields. Not Knowing what to do Sagara had only one idea left - to have himself and Kurtz distract the enemy force while Kaname makes a run to safety. But Kaname refuses to leave.

Sousuke suddenly decides to become Mizuki’s boyfriend! The cold, watchful eyes of Mizuki's friends settle firmly on Sagara - but it’s Kaname’s reaction he should be worrying about.

When Tessa rushes to an SDF base after hearing that an A21 member has been captured, she’s shocked to find Takuma Kugayama. Seina, at the controls of an RK-92, has an even bigger surprise waiting.

Kaname is in a bad mood after seeing Tessa emerge from the bath. Unfortunately, even as Sousuke Sagara tries to explain that things aren’t what they seem, Tessa finds a way to make the situation worse.

Kaname and Tessa are taken away! The gang follows the signal transmitted by Kaname’s bracelet to find them, but upon reaching their destination, they’re surrounded by the authorities.

The giant AS - Behemoth - is on the move, crushing Mao's M9 in only seconds! When Kurz attempts to engage the monstrosity, the situation looks bad - until a crusader appears in the sky!

Tessa and Mao decide the best way to settle a big argument is with an AS battle! While Mao is calm and composed, Tessa desperately seeks training from Sousuke.

Kaname, Sousuke, and the gang use summer break as an opportunity to visit the Narushino military festival, and during the annual AS competition, Sousuke helps give the underdog an advantage.

After learning that Gauron is still alive, Sousuke is ordered to join the Gauron Assassination Team. As he prepares for the mission, he has no idea the effect his actions will have on Tessa and Kaname.

The Mithril assault team finally begins to take Sousuke's advice into account, but it may be too late: Gauron has one of Sousuke's old comrades predicting what Sousuke will do.

Zaied outwits Sousuke's team and interdicts their advance! Zaied's team surrounds Sousuke's team who is carrying a nuclear warhead. Zaied moves first. While Sousuke is fighting against Zaied, Gray and the team are aghast at the power of Gauron.

Sousuke spends most of the budget for the school festival. Kaname gets so disappointed. It might have been his apology? He invites her to "go to a southern island", but the destination is not what she is thinking...

Flashbacks of Kurz and Sousuke's time as trainees.

The De Danaan is heading toward Melida Island when it receives an emergency contact. Gauron's troops have appeared at Beridaobu Island! This island is the US military's chemical weapons base. They have Gauron's new AS, Venom, rampaging around and also the latest mass production model, known as Shadow. Things start to get tense for Sousuke and the others.

Gauron manages to escape thanks to the betrayal of two soldiers. Gauron takes Kaname hostage and takes over Dana, the AI of the De Danaan.

Trouble brews on the Tuatha de Danaan. Gauron has taken control of Dana and isolated the crew into the back half of the ship. Tessa and Kaname are held prisoner on the bridge, helpless to stop Gauron.

Kurz and Sousuke, free to roam the mostly empty ship, fight to free the contained crew. Meanwhile, Gauron is getting desperate.

Kaname holds the ship together while Gauron and Sousuke face off. The problem is that Gauron knows he is beaten one way or the other. He plans to take everyone down with him.

A secret admirer leaves a love letter in Sousuke's shoe locker. Instead of finding the letter, he deduces that his locker was tampered with and promptly blows it up. From its fragments, Sousuke misinterprets the letter as a death threat and confronts his "stalker". Sousuke forgets Kaname's notes at home, and they make a frantic dash to retrieve them and return before lunchtime ends. Despite their tardiness, they find out that the notes were not needed since their teacher coincidentally fell sick.

During a day at the beach, Kaname becomes upset at Sousuke's insensitivity. When she goes off alone, she is asked to have tea with a boy who is enamored with her. Sousuke, however, believes that she was kidnapped and proceeds to rescue her from her apparent kidnappers.

During a field trip to the park, the class selects Sousuke to be the model for their art project. However, Sousuke misinterprets the modeling advice he receives from their art teacher, turning the assignment with his classmates into a game of life-and-death. Kaname goes on a date with a former classmate to an amusement park while Sousuke and Kyoko follow her. Sousuke seems relieved that she's simply on a date until a drunken yakuza group threatens Kaname. Not wanting to reveal that he was following her, Sousuke comes to the rescue disguised as the amusement park mascot.

Sousuke and Kaname ask the school's karate club to vacate their dojo, which is slated for demolition. However, the club refuses to leave, challenging Sousuke to a duel where they'll leave if they lose. Sousuke defeats the club's members with relative ease until he faces the club's captain. As a test of superiority, Sousuke and the karate club's captain compete to care for the injured school janitor; however, their overzealous efforts do more harm than good. The janitor tries to be patient, but finally goes berserk when they accidentally serve his prized koi pet to him for dinner.

Sousuke and Kaname investigate bizarre incidents where a masked predator attacks schoolgirls and gives them ponytails. With the help of a local policewoman, they set up a trap to catch the attacker using Kaname as bait. To teach a stoic Sousuke the meaning of fear, Kaname takes him into a haunted hospital, but she becomes more scared than Sousuke. They learn that the haunted hospital rumor was perpetuated by the mother and son living there who wanted peace and quiet.

To prevent the school from disbanding the rugby team, Sousuke and Kaname help train them for an exhibition match against a rival school. Upon discovering that the players are timid and passive, Sousuke subjects them to grueling basic training to toughen them up, which helps them win the match. The scene of Sousuke's grueling training of the rugby players by berating and abusing them to desensitize them to make them stronger references the boot camp scenes from Full Metal Jacket.

During a lull at the Mithril base after the events of the first season's final few episodes, Tessa decides to spend the time as an exchange student at Jindai High to learn more about school life. Sousuke, however, finds the stress of guarding her overbearing and collapses from fatigue.

Sousuke, Kaname, Tessa, Kurz, Melissa, and their friends travel to an onsen (hot springs) for some rest and relaxation before Tessa returns to Merida Island. Sousuke sets up a defensive perimeter and booby traps around the girls' bath, foiling the other boys' attempts to sneak a peek.

Sousuke and Kaname discover that Ren Mikihara is a yakuza daughter whose members ask for their help to deal with a rival gang. Sousuke, in his mascot disguise, trains the yakuza members. When the rival gang kidnaps Kaname and Ren, Sousuke and his recruits rescue them wearing the special mascot AS. The episode was dedicated to Kinji Fukasaku, director of Battles Without Honor and Humanity, who had died earlier that year.

A lack of space for all of Jindai High's student organizations prompts a review of each group's numbers. Because they only have two members, the social science club agrees to give up their room through a contest to see which club can recruit the most members of the opposite gender. Sousuke participates, but his poor social skills fail to attract anyone to his club. Kaname, feeling sorry for Sousuke, decides to help out so he can avoid a bet he made with another club.

Sousuke orders a new scope for his pistol, but receives a strange bottle instead. Unfortunately, the contents are a biological weapon. Even worse, the bottle is opened up in the school!

Mithril and the SRT rescue refugees caught in a civil war in the African country of Balic. However, during the fighting, they discover that the enemy possesses advanced weaponry rivaling their own. They surmise that a highly funded, well-equipped organization may be supplying their enemies.

Sousuke and Kazama investigate who is posting embarrassing and revealing pictures of Kaname on the internet. Meanwhile, Amalgam operatives led by Gates extract payment from the Balic military force that took on Mithril and try to reconstruct what happened in the battle.

In Nanjing, Amalgam kidnaps peace delegations from Northern and Southern China and fortify themselves in an underground tunnel beneath the Yangtze River. Mithril attempts a rescue in the tunnel's dangerous confines, but falls into Amalgam's trap.

Mithril is perplexed at how the enemy is able to follow their movements. Once they realize that their communications have been compromised, Tessa and Commander Andrei Kalinin give false orders to facilitate the rescue and turn the tables on Amalgam.

The SRT travels to Sicily to capture the traitor from the Nanjing operation. Sousuke has difficulties balancing work and school when he tries to have a phone conversation with Kaname and to drive a getaway vehicle at the same time. A mysterious AS also appears to help the team get away. Seeing the stress of his everyday duties, Mao decides to ask Sousuke about his own plans for the future.

Mithril attempts to learn more about the mysterious Amalgam organization. Sousuke and Kaname's relationship begins to blossom; however, the Mithril leadership forbids him from seeing her after his bodyguard duties are assigned to another agent.

Sousuke argues with his replacement, Agent Wraith, about the mission to protect Kaname. Kaname wonders why Sousuke has not been attending classes in days and starts to become worried. When she needs to see him after a chance encounter with Amalgam agent Xia Yu Lan, she finds his apartment vacant and he has disappeared.

After Sousuke arrives back at Merida Island, Tessa berates him for emotionally involving himself with Kaname and neglecting his other duties. Lt Belfangan Clouseau, the pilot of the AS seen in the Sicily operation, transfers to the SRT as its new commander. After he clashes with Kurz at the bar upon offending the memory of the SRT's dead comrades, Clouseau stages an AS duel to help Sousuke properly operate the Arbalest.

Kaname confronts Agent Wraith about Sousuke's departure, but as she is about to get answers, Xia Yu Lan ambushes the two. Kaname outwits her pursuer until Leonard Testarossa, another Amalgam agent who is also Tessa's brother, shows up and kills Xia Yu Lan. He reveals that the assassin was a rogue agent acting outside of Amalgam's interests.

Xia Yu Lan's twin sister, Yu Fan, hijacks a Venom AS to become an agent provocateur between the Northern and Southern Chinese Army units in Hong Kong. Sousuke and Melissa are deployed by Gavin Hunter to the area in a team of SRT/PRT personnel of East Asian origin to find the AS, but his feelings for Kaname nearly places the Mithril reconnaissance force in danger. After a tough sermon from Melissa touches a raw nerve, Sousuke deserts the team.

Sousuke continues to wander in Hong Kong and encounters a prostitute who looks very much like Kaname. Tessa is "forced" by Admiral Jerome Borda to deploy Clouseau, Melissa, and Kurz to the island after sightings of the Venom AS are confirmed.

Xia Yu Fan leads Sousuke to Gauron while she runs off to fight Clouseau, Melissa, and Kurz in Hong Kong as Northern and Southern China teeter on the brink of hostilities. Now crippled and about to die, Gauron explains the truth about Amalgam and taunts Sousuke by claiming to have killed Kaname because it changed him into someone weak. Enraged, Sousuke kills Gauron and gets out of the building just as a bomb under his bed explodes. Gates and his Amalgam team also arrive to kill Xia Yu Fan. Tessa launches the Arbalest despite Mithril's orders not to.

Still demoralized by Gauron's claims of killing Kaname, Sousuke still refuses to function until Kaname finally appears to get him back on his feet. Inspired by her presence, Sousuke pilots the Arbalest again to destroy Gates and his men. Kaname returns home to Japan. Sousuke faces the Mithril command, which grants his request to stay with Kaname even if his wages are reduced.

Amalgam decides it's time to get serious about its Mithril problem, and this means big challenges are on the horizon for Sousuke, Kaname, and Tessa. As enemies close in on all fronts, will they find ways to overcome those challenges?

In Tokyo, Sousuke and Kaname flee from enemy agents in a desperate attempt to rendezvous with their allies. On Merida Island, Mithril struggles to respond to a fierce and demoralizing assault by Amalgam forces.

The SRT team has its hands more than full trying to protect Merida Island from three rampaging Behemoths. Sousuke and Kaname attempt to deal with their own frantic situation, as Amalgam's Kurama drags the students of Jindai High School into the fray.

Sousuke and Kaname work together to save Kyoko and everyone else at Jindai High, and they both reach a point where they must make difficult, fateful decisions. Tessa likewise tries to save as many of her people as possible as she abandons the island base.

Sousuke makes his way to the city of Namsac, where people bet on fighting matches between decommissioned Arm Slaves. Thanks to a bit of serendipity, he meets a team owner named Nami at the arena just when she's looking for an AS operator.

While enjoying considerable success fighting in the arena for Nami's team, Sousuke starts to grow accustomed to his new life in Namsac. But little things keep reminding him he came to this city with a specific purpose in mind.

The Crossbow team takes part in their first illegal battle, but nefarious forces are at work behind the scenes. If Sousuke doesn't play his cards right, this first battle could end up being his last.

Sousuke's grudge against Kurama escalates into a full-blown shooting war on the streets of Namsac, but is it possible for him to fight this war all by himself? And every war has its share of casualties.

When Tessa is found wandering dazed and barefoot on a California highway, her attending psychiatrist just might be in for the case of a lifetime. The story Tessa tells sounds like an intricate delusion, but sometimes truth is stranger than fiction.

Sousuke who are attacked by amalgam. Raids also come closer to Sousuke who cannot heal wounds yet. On the other hand, Tessa who missed Fowler slightly afterward pledges Leonard and amalgam.

Lemon determines where Kaname is likely being held captive, so Sousuke and his ragtag group launch a rescue mission. But many forces are on the move this stormy night, and the mission doesn't quite go according to plan.

Leonard and Kalinin make every effort to spirit Kaname away before Sousuke can reach her. As battle erupts between rival Amalgam factions and Mithril remnants, Sousuke and Kaname both find they have to fight against fate to hold on to hope.