With the earth alliance weakened, Haruo weighs siding with the Exif, whose death cult is summoning a monster that can destroy the world.

On Earth, Haruo and his companions make contact with the indigenous Houtua tribe. To defeat Godzilla, they set out for the old Mechagodzilla facility.

A desperate group of refugees attempts to recolonize Earth 20,000 years after Godzilla took over. But one young man wants revenge above all else.