The story follows humans as they struggle to survive against the threat of the shapeshifting gigantic alien monsters called Gauna (奇居子?). The manga begins a thousand years after humans flee from Earth, which was supposedly destroyed by the Gauna, aboard massive spaceships created from the remains of the planet. The Gauna follow the emigration ships into space, forcing the humans to create large mechanized weapons called Guardians (衛人 Morito?) to protect themselves. Most people in the surviving human population are screened and drafted as Guardian pilots at a young age, if they are shown to be capable of piloting the mecha. The story focuses on one of such ships named Sidonia which has developed its own human culture closely based on that of Japan where human cloning, asexual reproduction and human engineering such as controlled hybrid human/animal mutations and human photosynthesis are commonplace.