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.

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 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!

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.

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.

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.

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.

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 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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.