A thousand years ago, our solar system was destroyed by gigantic shapeshifting-aliens called Gauna. The human race created massive spaceships before it, they each voyaged to find a planet where they can live in peace. This story is one of spaceship named Sidonia fights against Gauna, with the central focus on Nagate Tanikaze who is a enigmatic teenage boy becomes one of pilots of guardian-robots, and grows up to be Flying Ace called "Knight of Sidonia".