Full Metal Panic? Fumoffu

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!