At the south pole, the EDF (Earth Defense Force) face off against Godzilla. They trap him in the ice, using the EDF's best weapon: The Gotengo, freezing him. Decades later, the EDF discover a mummified Gigan. A mutant soldier, Shinichi Ozaki and biologist Miyuki Otonashi are sent to research it. The Shobijin, Mothra's twin fairies, reveal to them that the mummified monster is Gigan, an alien cyborg sent to destroy Earth 12,000 years ago, and that soon, a battle between the forces of good and evil will come.
Suddenly, monsters appear all over the Earth. Anguirus attacks Shanghai, China. Rodan attacks New York City, USA. King Caesar attacks Okinawa, Japan. Kamacuras attacks Paris, France. Kumonga attacks Arizona, USA. Zilla attacks Sydney, Australia, and Ebirah attacks a factory near Tokyo, Japan. Soon after, the monsters disappear as a giant UFO appears over Tokyo. The aliens reveal themselves as the Xillans, who befriend them. They warn Earth of an asteroid called Gorath will soon attack Earth. Soon after, the Xillens betray Earth and set the monsters loose on Earth once more. Gigan is also revived and joined in to destroy the Earth.
Meanwhile, in Mt. Fuji, a hunter and his grandson, named Kento, discover Minilla, who is discovered to be Godzilla's son. The trio escape the Xillen's wrath and stay low, attempting to keep a low profile. The EDF decide to make a very risky move: thaw Godzilla from the ice. They travel to the South Pole in an attempt to free him from the ice, but are stopped by Gigan, who is unable to stop them from freeing Godzilla. Godzilla roars in awakening from his icy prison, and has a brief encounter with Gigan, destroying him by blasting his atomic breath into Gigan's head, blowing it up. Godzilla then turns to the Gotengo, and attempts to destroy it, but it flies away and Godzilla follows, unwittingly saving the Earth in the process.
First, Godzilla arrives in Sydney, Australia and encounter Zilla, who is killed in literally 11 seconds. Zilla sprints towards Godzilla, who shoots his atomic breath at it, but Zilla jumps just in time, but Godzilla swings its tail at it and slams Zilla into the Sydney Opera House, then blasts its atomic breath, destroying both Zilla and the opera house. Later, he encounters Kumonga, then Kamacuras, then later, he battles King Caesar, Anguirus, and Rodan all at the same time on Mt. Fuji. He does not kill them, probably due to the fact that all of them were previously Godzilla's allies. Later, Godzilla fights Hedorah and Ebirah, who are killed in a very short battle.
Gorath falls down to Earth, but Godzilla destroys it, however, a powerful space dragon, Monster X, was inside the meteor. A great battle ensues, until Gigan comes to aid Monster X, but later, Mothra comes to aid Godzilla. Mothra sacrifices herself to kill Gigan, while Godzilla is still fighting Monster X. Meanwhile, in the Xillen mothership, the humans/mutants confront the aliens, and have a battle. Eventually, the humans win when Ozaki unleashed his Kaiser powers and kills the leader. While back on the surface, Monster X transforms into the terrible beast, a giant three-headed dragon known as Keizer Ghidorah, and after a long battle, Godzilla emerges as the victor. Then Godzilla turns and gets ready to kill the humans, until at the last second, Minilla convinces Godzilla not to, then they walk into the ocean, and Godzilla roars in triumph.
During the credits roll, Hedorah is shown emerging from the wreckage from his battle with Godzilla, showing that he survives, and Mothra flies back to Infant Island, suggesting she survived as well.
Godzilla: Final Wars contains a very large list of kaiju.
- Godzilla, The main hero of the film. He is known as the King of the Monsters.
- Anguirus, He appears as one of the many controlled monsters. He attacks Shanghai, China.
- Mothra, She appears as Godzilla's ally and aids him in the final fight against Gigan and Monster X.
- Rodan, He usually appears as Godzilla's ally, but is a controlled monster and is shown attacking New York City, USA.
- Ebirah, Its first official appearance (not counting his appearance in All Monsters Attack), was in Godzilla vs. The Sea Monster (1966), and is seen attacking a factory near Tokyo, Japan.
- Minilla, Minilla is Godzilla's son, and travels with a boy named Kento, and his grandfather.
- Kumonga, a giant spider who is controlled by the aliens and attacks Arizona, USA.
- Kamacuras, a giant praying mantis who is also a controlled kaiju and attacks Paris, France.
- Manda, He only makes a cameo fighting the Gotengo, in London, England.
- Hedorah, a giant blob of pollution who fights Godzilla alongside Ebirah.
- Gigan, one of the main villains who has hooks for hands and a buzzsaw on his chest. After having his head blown up, the aliens repair him and upgrade him with chainsaw hands.
- King Caesar, first appears in Godzilla vs. Mechagodzilla (1974), and is one of the many controlled aliens and attacks Okinawa, Japan (which is ironic because he is the protector of Okinawa.)
- Zilla, Zilla was killed in 11 seconds by Godzilla, making it a record for the shortest Godzilla battle. It is also controlled by the Xillens and attacks Sydney, Australia.
- Monster X, a monster who emerges from a meteor and is considered by some fans as Godzilla's greatest opponent.
- Keizer Ghidorah, the second form of Monster X, who nearly kills Godzilla, but Godzilla gains the upper hand and kills Keizer Ghidorah.