The film is a compilation of all 12 episodes of the first season with new sequences and redone sound effects.

Outer space, the far future. 
A lone seed ship, the Sidonia, plies the void, ten centuries since the obliteration of the solar system. The massive, nearly indestructible, yet barely sentient alien life forms that destroyed humanity’s home world continue to pose an existential threat. 
Nagate Tanikaze has only known life in the vessel’s bowels deep below the sparkling strata where humans have achieved photosynthesis and new genders. Not long after he emerges from the Underground, however, the youth is bequeathed a treasured legacy by the spaceship’s coolheaded female captain. 
Meticulously drawn, peppered with clipped humor, but also unusually attentive to plot and structure for the international cult favorite, Knights of Sidonia may be Tsutomu Nihei’s most accessible work to date even as it hits notes of tragic grandeur as a hopeless struggle for survival unfolds.
 
(Source: Kodansha USA)

It's been a thousand years since the Gauna, a strange alien race with no known method of communication, 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. When he goes into training to pilot the huge robotic weapons known as Gardes, Nagate is entrusted with piloting the legendary unit known as Tsugumori. Nagate and his fellow pilots put their lives on the line against the Gauna, in the ultimate battle for the survival of humanity! 
(Source: AniDB)

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