In the distant future, mankind is divided into two factions: Union and Deague. They have waged a war against each other for so long that no one remembers when it first began. The backbone of the Union military is the manned weapons system Strain, while the Deague uses an unmanned version, the Tumoru. Sara Werec, the daughter of a respectable family, is a 16-yearold girl who attends Grapera Space Armed Soldier Academy located in the Cranial Solar System, where she is training to become a full-fledged Reasoner (a Strain pilot). Her brother, Ralph Werec, had been sent to the frontline 130 light-years away to accomplish a special mission when she was 11 years old, a distance that requires 400 years of objective time to traverse by even the fastest Union spacecraft. However, in accordance with the theory of relativity, this corresponds to only two subjective years (time as experienced by those within the spacecraft). The two of them had lost their parents when they were young and the bond between the two is very close. It is Sara’s dearest wish to be reunited with her brother. To do that, she must travel to the battlefield where he is. One day, Sara’s planet is suddenly assaulted by Deague forces. To her surprise, her brother, Ralph, turns out to be one of the raiders who successfully kidnap a mysterious girl sleeping in a capsule. In order to find the truth, Sara gets in a Strain and chases after him. However, she is attacked by Ralph, and the Mimic, a copy of the pilot’s brain which is essential to controlling the Strain, is damaged.

Eleven-year-old Sara Werec's elder brother, Ralph, was sent to the frontlines of an interstellar war 130 light years away, and Sara vowed to reunite with him one day as a comrade. Five years later, Sara is a student at Grapera Space Armed Soldier Academy, training to become a Reasoner, a pilot of an advanced weapons system called a "Strain." When the academy is suddenly attacked by enemy forces, Sara enters battle against a Strain that quickly overpowers her. After incapacitating her, the pilot reveals himself to be her Ralph. Killing all the other students and destroying the school, he disappears, leaving Sara to question everything she has ever known. Soukou no Strain is the story of Sara as she reenters training under a new name, now determined to confront her brother and make sense of her brother's actions.

Taking place after the events of Heaven and Earth and before Exodus, Behind the Line depicts the moments of boys and girls after Soushi Minashiro returned home.

Tatsumiyajima is the central island in the middle of a small cluster of islands, in a sleepy backwater of the Japanese isles. Not much happens there, and the island's young people go to school knowing that their lives are likely to remain peaceful and undisturbed. Or so they have been taught... but the truth is different. The fate of mankind is on the line, and Tatsumiyajima is the last line of defense against a hostile and incomprehensible enemy. At the center of it all, fighting for Humanity's continued existence, is the giant robot Fafner, the dragon that guards this final treasure of mankind.