Nagate Tanikaze lived secretly the bottom of spaceship named Sidonia. One day, he broke the will of his grandfather, and goes to the upper floor for food.
It has been decided that a group of unarmed neutralism settle in Seventh Planet of the Lem Star System. Meanwhile, Izana Shinatose and Yuhata Midorikawa each asks Nagate for a trip.
All of Morito have to attack the main body in the Gauna until Anti-planet Homing Missile will reach it. Also Beni-Suzume appears, the fight is confusing and chaotic.