Three years prior, a global war erupted due to an alien invasion. The protagonist, Takushi, a soldier who was conscripted at the start of middle school, has just been discharged after the aliens were defeated. He is concerned about his academic skills, having only fought for three years, and whether he can re-enroll in school. He is approached by Natalie, a fellow soldier and friend, who speaks Japanese. Natalie's hometown was destroyed, and she asks to live with Takushi in Japan. Despite his reservations about her ruthless combat style and persistent, somewhat manipulative personality, Takushi agrees, partly because she saved his life multiple times, but insists on splitting living expenses.
Takushi's discharge is complicated by his superior's reluctance to let Natalie, a highly skilled soldier, leave. Natalie insists on staying with Takushi, leading to him being placed on indefinite leave instead of fully retiring. On the plane to Japan, Takushi expresses his frustration at being tied to the military, while Natalie playfully teases him about their "new life."
Upon arriving in Takushi's hometown, which was thankfully spared from the war, he warns Natalie to behave. She, however, continues her playful and often inappropriate remarks, much to Takushi's exasperation. Meanwhile, Takushi's older sister, who has been living in constant fear of receiving news of his death, is visited by Takushi and Natalie. The reunion is overwhelmingly emotional for his sister, who had given up hope of seeing him alive.
Takushi's sister is shocked by Natalie's bold declaration of being married to Takushi, which he quickly dismisses as a misunderstanding, explaining Natalie is a war comrade with nowhere else to go. The family then goes out to eat, where Takushi explains the psychological toll of the war and how soldiers clung to hopes of a normal life, like dating, to cope with the constant threat of death. He also reveals that he and Natalie were biologically modified by the military to fight the aliens, a fact he kept from his parents to spare them further worry.
The next day, Takushi and Natalie are studying for their high school entrance exams at a department store. Takushi's sister, Hana, is worried about them attending her high-ranking school with their academic deficiencies. Suddenly, a notorious bully named Oogami Tenga appears and harasses Hana. Natalie intervenes, and Takushi, realizing the situation is escalating, leads them to a secluded area. Tenga and his thugs follow, intending to attack. Takushi, demonstrating immense strength, incapacitates Tenga and his men, forcing them to agree to leave Hana alone and relocate.
A week later, Takushi and Natalie pass their entrance exams. Hana confronts Takushi about his enhanced abilities, and he explains he and Natalie were genetically modified by the military. Hana, though initially shocked, accepts him and expresses gratitude for his sacrifice. They decide to start a normal high school life, unaware of the chaotic future that awaits them, including encounters with former comrades, a famous singer, and further complications arising from their military modifications.