Após conseguirem os meios para continuarem pela busca da salvação para seu povo e provavelmente toda a humanidade, Kaina e Ririha partem para atravessar a grande fossa oceânica e se aventurarem em terras desconhecidas.
The catastrophe "Skyfall" was brought by the collapsed orbital space colony crashed into the Earth. Inside the crater at the crash site now inhabit Kaiju born by gene mutation. Ray, an avatar, comes to the area to collect the scattered "seeds", not knowing what really is going on there, He soon meets Mil, a mysterious girl. Is she a human, or a Kaiju?
After the Earth was destroyed by mysterious alien lifeforms known as the Gauna, surviving remnants of the human race escaped to space in the enormous generation ship Sidonia. Having drifted through space for millennia, the Sidonia found itself once more under attack from Gauna for the first time in a century. Once again facing the threat of extinction, a temporary victory against the Gauna was eked out thanks to the human-Gauna hybrid Tsumugi Shiraui and ace Guardian mech pilot Nagate Tanikaze. 10 years later... The people of Sidonia enjoy a brief respite. Peaceful days pass, during which Tsumugi begins to realize her feelings for Nagate, who is now celebrated as a hero of Sidonia. However, as Captain Kobayashi has always known, as long as the Gauna remain, peace cannot last. The decision is made: a final battle, upon which rests the fate of humanity's last survivors. As the end approaches, will the crew be able to protect those they love?
No século XX, a humanidade soube da existência do Godzilla e, após diversas derrotas, fez um plano para sair da terra e habitar outro planeta. Porém, os cálculos estavam errados e após uma viagem de 20 anos, os humanos perceberam que o planeta escolhido não tinha condições para a vida. O protagonista da trama é Haruo, que viu seus pais serem mortos pelo Godzilla quando tinha 4 anos e agora só quer voltar para a Terra e derrotar o animal. Ao voltarem, no entanto, já se passaram 20.000 anos na Terra, que agora tem seu ecossistema controlado pelo Godzilla.
