太陽系が奇居子（ガウナ）と呼ばれる謎の生命体によって破壊されてから1000年後の世界。人類の繁殖と生産を維持しながら宇宙を旅する播種船・シドニアに暮らす主人公、谷風長道が人型兵器「衛人」の操縦士訓練生となり、仲間とともにガウナとの戦闘を繰り広げる。
A recap of the first season of Sidonia no Kishi with additional scenes and re-edited sound effects.
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?