Core exposed. Outer space, the far future. A lone seed ship, the Sidonia, plies the void, ten centuries since the obliteration of the solar system. The massive, nearly indestructible, yet barely sentient alien life forms that destroyed humanity's homeworld continue to pose an existential threat.

Nagate Tanikaze has only known life in the vessel's bowels deep below the sparkling strata where humans have achieved photosynthesis and new genders. Not long after he emerges from the Underground, however, the youth is bequeathed a treasured legacy by the spaceship's coolheaded female captain.