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.

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.