A thousand years after humanity fled Earth from the shape-shifting Gauna, the seed ship Sidonia drifts through deep space carrying a culture that clones its citizens and photosynthesizes its food. Nagate Tanikaze, raised underground and trained only on an old simulator his grandfather built, is conscripted into the Garde mecha corps just as a new Gauna closes on the ship. His squadmates, among them the third-gender pilot Izana Shinatose and the ace Shizuka Hoshijiro, draw him into Sidonia's defense.