Nagate Tanikaze trains to become a Garde pilot and defend the Sidonia from a hostile alien species called Gauna.

10 years have passed since the last episode of TV series, Sidonia's crew have carefully prepared for the big war with non-interactive creature, Gauna, in order to settle in the planet seven in Lem star system. The ace of aces Nagate comes to love Tsumugi dearly. However, the malice of an old scientist lurking in a guy changes the entire situation.