Using the fossil of the Legendary Pokémon Mew, Team Rocket has created the first successful Pokémon clone. Named Mewtwo, the man-made Pokémon quickly becomes upset with the circumstances of its creation and goes on a rampage. It is soon approached by Sakaki, the leader of Team Rocket, and is manipulated into committing evil acts. Repulsed by the tricks of mankind and the cruelties it has suffered, Mewtwo isolates itself from everyone and plots against humans whilst trying to discover its true purpose in life. Disguising as the world's strongest Pokémon trainer, Mewtwo draws in the region's most powerful trainers who want to fight the new, mysterious opponent. With the fate of the world at stake, renowned trainers Satoshi, Takeshi, and Kasumi must battle against Mewtwo and defeat it before it brings about the downfall of humanity.

Air Trecks, also known as AT, are motorized and futuristic inline skates that are the new craze taking the nation by storm. Although each AT comes with a speed limiter, a community of daredevils known as the Storm Riders are brave enough to tamper with the device. Utilizing AT's in underground battles, individual teams wager valuable AT parts or team emblems—their symbol of pride—to dominate the streets. Living in this era is Itsuki Minami, a middle school student notorious for engaging in street fights. Always wanting to reach heights no one else is able to, the reckless punk will break through any obstacle that stands in his way, alongside his best friends Kazuma Mikura and Onigiri. However, it is when he discovers a pair of Air Trecks in his house that the path to his true desire finally opens: to rule the skies.

Sergeant Sousuke Sagara returns to Jindai High School to protect the precious war asset, Kaname Chidori, from any threat. However, his lack of social skills and real-life experience result in comical yet dangerous situations, endangering the peaceful school life Kaname longs for. As Sousuke continues to bring a wide range of weapons to school as a means to solve threats—real or fake—Kaname struggles to fulfill her duty as the student council vice president all while keeping him in check. To ensure a successful mission, Sousuke is occasionally forced to use the costume of a famous amusement park mascot called Bonta-kun. With his technical expertise, he eventually transforms the exuberant uniform into a cutting-edge exoskeleton that has only one dysfunction: the voice translator can only produce the sound mofu. Full Metal Panic? Fumoffu depicts the adventures of Kaname and Sousuke as they try to live their normal school lives despite the chaos they inadvertently cause.

From an early age, Haruka Sakura was made an outcast due to his unconventional appearance and lack of social skills. However, the rough treatment turned him into a proficient fighter, which is now the only thing he prides himself on. Starting at Furin High School, where it is rumored that strength is valued over academics, Sakura has only one goal—taking the top spot. Involved in a street brawl the day before his enrollment, Sakura happens to meet a group of his future schoolmates. Instead of the usual rejection, they fight alongside him, demonstrating that what the school actually cares about is protecting the town of Makochi from any harm—hence why the students call themselves Bofurin. Surprised by the support and appreciation of the townspeople, Sakura has a hard time accepting their goodwill. Though unfamiliar with kindness being shown to him, Sakura must learn to push past his discomfort when Bofurin is pitted against formidable enemies. After experiencing the feeling of acceptance, he finds himself fighting for the sake of others for the first time.