Endless warfare and environmental pollution had resulted in the creation of monsters and the Earth Defense Force (EDF) is established to protect the planet. The organization is equipped with the best technology, weapons and soldiers, as well as mutants with special abilities. Godzilla is the EDF’s only unstoppable opponent. The EDF’s best combat vehicle, the Gotengo, corners Godzilla at the South Pole and buries it under the Antarctic ice, freezing it alive.
Forty years later, the EDF discovers a mummified space monster. The mutant soldier Shinichi Ozaki and the United Nations biologist Dr. Miyuki Otonashi are sent to research it. Shortly thereafter, the two encounter the Shobijin, fairies of the guardian monster Mothra, who reveal that the monster is Gigan, an alien cyborg sent to destroy Earth 12,000 years earlier. They also warn that a battle between good and evil will happen soon and that Ozaki, because of his mutant capabilities, must choose between the two.
Suddenly, monsters appear in major cities. The EDF engage the creatures but mysteriously vanish at the same moment when an enormous alien mothership appears over Tokyo. The aliens, known as Xiliens, warn the world of an incoming asteroid called “Gorath” will soon collide with Earth. Because of their peaceful nature, the UN is disbanded and the Space Nations, an alliance to unite the universe, is organized.
Ozaki, Miyuki, and several others distrust the Xiliens and together discover that the Xiliens are actually the ones who unleashed the monsters and have also replaced several members of the EDF with duplicates. After exposing their true intentions on television, the Xiliens unleash the monsters once more and destroy the rest of civilization.
On Mt. Fuji, a hunter, Samon Taguchi, and his grandson, Kenta, discover Minilla, Godzilla’s son. They are successful in keeping a low profile and hiding from the Xiliens’ assault.
Gordon proposes freeing Godzilla to allow him to defeat the other monsters. Using the Gotengo, the surviving EDF members travel to Antarctica and unleash Godzilla, who engages Gigan in battle after following the Gotengo. The Gotengo then leads Godzilla across the Pacific to battle the other monsters. Gotengo then returns to Tokyo to engage the Xiliens.
Godzilla destroys Gorath before it crashes, unleashing Monster X. Gigan, who has now been revived and upgraded, aids Monster X, but Mothra arrives to counter it into battle. Inside the Xilien mothership, the humans confront the Xilien Regulator. Ozaki is revealed to be a “Keizer”, an all-powerful being capable of controlling Earth. Deciding to stay with the humans, Ozaki fights the Xilien Regulator, who is also a Keizer. After an extended battle, the humans are victorious and flee the mother ship’s destruction.
With Gigan and Mothra dead, Godzilla continues his battle with Monster X, who transforms into Keizer Ghidorah. Keizer Ghidorah initially has an advantage over Godzilla but Godzilla emerges victorious after Ozaki transfers his Keizer energy to the monster. Godzilla then turns to finish off the Gotengo, but Minilla arrives, along with the hunter and his grandson, and blocks Godzilla from harming the humans, which causes Godzilla to realize that he must forgive mankind. The survivors watch as Godzilla and Minilla peacefully return to the ocean.