Many years ago, the Gauna aliens destroyed Earth and have relentlessly pursued humanity's remnants. These survivors narrowly escaped and fled across the galaxy on giant seed ships. In the year 3394, Nagate Tanikaze emerges from lifelong seclusion on the seed ship Sidonia in search of food, only to be unwittingly thrust into unfolding events. As the Gauna launch their assault on Sidonia, Tanikaze, aided by comrades Shizuka Hoshijiro, Izana Shinatose, and Yuhata Midorikawa, must defend humanity's last hope and defeat the alien aggressors. Tanikaze's journey continues as he discovers the unknown world above him and becomes the hero that Sidonia desperately needs.