Commencement.Deep within the massive spaceship Sidonia, a hungry Nagate Tanikaze ventures outside his underground shelter, but he ends up arrested for stealing manufactured rice and admitted to the hospital for his injuries. Although managing to escape the hospital, Nagate is subdued by an arrogant Norio Kunato, before he is taken to the police station by Shizuka Hoshijiro. Instead, Ochiai escorts Nagate to see Captain Kobayashi, who proposes him to become a Garde pilot through a cadet training program for Type 18 Gardes. Nagate befriends Izana Shinatose, an intersex third gender whose body can adapt after finding a mate. The training program teaches that the main mission is to defend Sidonia against a hostile alien species called Gauna, which destroyed Earth in the distant past but have not been seen in a century. Nagate is later called to his first sortie, and he is entrusted with Tsugumori, a legendary Type 17 Garde that belonged to a famous war hero, since its controls are similar to his Garde virtual training console in his shelter. While the cadet squads perform a mining expedition at a nearby asteroid, Gauna 487 suddenly erupts beneath the surface, leaving Nagate severely injured and Tsugumori heavily damaged.