Misery seems everlasting in Miyo Saimori's life. Born from an arranged marriage, she was quickly discarded after her mother's tragic death. Her father remarried, and her younger half-sister Kaya received all the affection, while Miyo was degraded to a lowly servant. Lacking the strength to fight against her family's abuse, Miyo loses hope that her luck will ever turn. Unexpectedly, Miyo's father summons her to deliver surprising news: she is to marry Kiyoka Kudou, the head of the distinguished Kudou family. Despite his noble background, Kiyoka is known to be a callous man who has thus far dismissed all of his former fiancées. Upon arriving at the Kudou household, Miyo expects coarse treatment and to be tossed aside. However, contrary to her assumptions, Kiyoka shows her the kindness and love that she has desperately needed. Marrying Kiyoka may be Miyo's one chance to break free from her neglectful family and embrace a life of happiness.

In the distant future, a majority of humans have left the Earth, and the Galactic Alliance of Humanity is founded to guide exploration and ensure the prosperity of mankind. However, a significant threat arises in the form of strange creatures called Hideauze, resulting in an interstellar war to prevent humanity's extinction. Armed with Chamber, an autonomous robot, 16-year-old lieutenant Ledo of the Galactic Alliance joins the battle against the monsters. In an unfortunate turn of events, Ledo loses control during the battle and is cast out to the far reaches of space, crash-landing on a waterlogged Earth. On the blue planet, Gargantia—a large fleet of scavenger ships—comes across Chamber and retrieves it from the ocean, thinking they have salvaged something of value. Mistaking their actions for hostility, Ledo sneaks aboard and takes a young messenger girl named Amy hostage, only to realize that the residents of Gargantia are not as dangerous as he had believed. Faced with uncertainty, and unable to communicate with his comrades in space, Ledo attempts to get his bearings and acclimate to a new lifestyle. But his peaceful days are about to be short-lived, as there is more to this ocean-covered planet than meets the eye.

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.

For 500 years, the Taboo Emperor, Arthur Gaz, ruled the Gaz Empire with an iron fist and conducted inhumane experiments on his own people. But his reign came to an end five years ago, when mighty warriors—later known as the Eight Heroes—defeated him in a battle for the capital. His death ended the 300-yearlong war between the Gaz Empire and the alliance of six nations. In the present day, Tooru Acura is a former saboteur from the war who has difficulty settling into the peaceful world, as he cannot find a job where he can put his fighting skills to use. An opportunity appears before him, however, when he meets a white-haired Wizard named Chaika Trabant. With a coffin on her back, she is searching for the scattered remains of her father in order to give him a proper burial, and she hires Tooru and his adoptive sister Akari to help her. However, the six nations alliance, which have now formed the Council of Six Nations, dispatches Albéric Gillette and his men from the Kleeman Agency to pursue and apprehend the late Emperor Gaz's daughter—Chaika. With the shocking revelation of Chaika's identity, the Acura siblings must choose between helping her gather the remains of the tyrannical emperor and upholding the peace the continent strives to maintain.