It's been 1,000 years since the Gauna destroyed the solar system. A portion of humanity managed to escape using enormous "seed ships" like the Sidonia, which have allowed them to maintain the population while drifting through space. Nagate Tanikaze is a young man who has been raised deep in the bowels of the ship. Nagate goes into training and is entrusted with piloting the legendary unit known as Tsugumori. Nagate and his fellow pilots put their lives on the line against the Gauna!