The year is 3394. The solar system has been long destroyed by a strange alien race called Gauna. Now humans are barely maintaining population in their seed ships - the ones they also used to escape a thousand years ago. After several years of drifting though space, Sidonia, a seed ship with a population of over 500,000 people, is once again threatened by Gauna. Follow Tanikaze Nagate, a mysterious young man from the deep corners of the ship, and his friends as they try to strike back against these gigantic creatures and at the same time learn what they really are for the sake of humanity's survival. -MAL

After the Earth was destroyed by mysterious alien lifeforms known as the Gauna, surviving remnants of the human race escaped to space in the enormous generation ship Sidonia. Having drifted through space for millennia, the Sidonia found itself once more under attack from Gauna for the first time in a century. Once again facing the threat of extinction, a temporary victory against the Gauna was eked out thanks to the human-Gauna hybrid Tsumugi Shiraui and ace Guardian mech pilot Nagate Tanikaze. 10 years later... The people of Sidonia enjoy a brief respite. Peaceful days pass, during which Tsumugi begins to realize her feelings for Nagate, who is now celebrated as a hero of Sidonia. However, as Captain Kobayashi has always known, as long as the Gauna remain, peace cannot last. The decision is made: a final battle, upon which rests the fate of humanity's last survivors. As the end approaches, will the crew be able to protect those they love?