The year is 3394. The solar system has been long destroyed by a strange alien race called Gauna. Now humans are barely maintaining population in their seed ships - the ones they also used to escape a thousand years ago. After several years of drifting though space, Sidonia, a seed ship with a population of over 500,000 people, is once again threatened by Gauna. Follow Tanikaze Nagate, a mysterious young man from the deep corners of the ship, and his friends as they try to strike back against these gigantic creatures and at the same time learn what they really are for the sake of humanity's survival.
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