20,000 years in the future on Earth, Godzilla is at the top of the ecosystem, and humans fight to take back the planet.
On Earth, kaijuu suddenly appear, and the ultimate being of Godzilla rises to exterminate them. After half a century of war between Godzilla and the kaijuu, humanity devises a plan to escape the planet. A group of humans chosen by AI board a spaceship called Aratram to travel 11.9 light years to immigrate to a new planet, Tau Ceti e, which rotates around the star Tau Ceti in the constellation Cetus. After traveling for 20 years, the ship barely makes it to the new planet, only to find that it can't support human life.
The protagonist is Haleo, who saw Godzilla kill his parents before his eyes when he was four years old. During the 20-year voyage, he has thought only of going back to Earth and killing Godzilla to avenge his parents. He joins a team that will conduct a dangerous trip through hyperspace to return to Earth. However, when they arrive, they find that 20,000 years have passed on Earth, and the world they once knew has completely changed.