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?

In the distant technological future, civilization has reached its ultimate Net-based form. An “infection” in the past caused the automated systems to spiral out of order, resulting in a multi-leveled city structure that replicates itself infinitely in all directions. Now humanity has lost access to the city’s controls, and is hunted down and purged by the defense system known as the Safeguard. In a tiny corner of the city, a little enclave known as the Electro-Fishers is facing eventual extinction, trapped between the threat of the Safeguard and dwindling food supplies. A girl named Zuru goes on a journey to find food for her village, only to inadvertently cause doom when an observation tower senses her and summons a Safeguard pack to eliminate the threat. With her companions dead and all escape routes blocked, the only thing that can save her now is the sudden arrival of Killy the Wanderer, on his quest for the Net Terminal Genes, the key to restoring order to the world.