In 1996, after the death of SpaceGodzilla, Miki Saegusa travels to Birth Island to check on Godzilla and his adopted son, but finds the entire island destroyed. Godzilla appears in Hong Kong, covered in glowing lava-like rashes. He goes on a rampage, causing major collateral damage and killing thousands of civilians. A group of representatives from the Japan Self Defense Forces (JSDF) hires college student Kenichi Yamane, the grandson of Dr. Kyohei Yamane, to work at the center in an attempt to unravel the mystery of Godzilla’s condition. Yamane suspects that Godzilla’s heart, which acts as a nuclear reactor, is going through a nuclear meltdown. He theorizes that, when Godzilla’s temperature reaches 1,200 degrees Celsius, he will explode with a force approximately “1,000 times greater than all nuclear weapons put together, a burst of power unseen since time began.”
The JSDF deploys a flying combat vehicle outfitted with anti-nuclear cold weapons, the Super-X III. Meanwhile, scientists create a new formula for the Oxygen Destroyer that was created by Dr. Serizawa in 1954. The JSDF fears that the Oxygen Destroyer, which was used to kill the original Godzilla, may have disastrous side effects, which is proven when a colony of Precambrian organisms is discovered to have been mutated by the formula. The creatures infest a sewer network and make their way into an aquarium, killing all the sea life inside. They rapidly evolve into monstrous crab-like creatures and begin wreaking havoc. After several deadly skirmishes with the JSDF, the creatures, dubbed “Destoroyah”, evolve beyond the military’s containment abilities.
Little Godzilla, who reappears as Godzilla Junior, having mutated further and now closely resembling his father, heads for the island where he was born. Godzilla, searching for his son, follows him, but complications arise. Due to his encounter with the Super-X III, Godzilla will not explode, but will instead suffer a bodily meltdown. After the meltdown, Godzilla’s superheated remains will bore into the planet’s core, destroying the Earth. Desperate, the JSDF works to lure Godzilla into a confrontation with the evolving Destoroyah by hiring Miki and another psychic named Meru Ozawa into telepathically instructing Junior to travel to Tokyo, which Destoroyah is currently invading. Godzilla will likely follow and, since Destoroyah was born from the same weapon that destroyed the first Godzilla, he will lose the battle, preventing the meltdown.
The psychics successfully lure Godzilla Junior to Tokyo, where he is attacked by Destoroyah, who has now increased in size and sprouted a pair of bat-like wings. In the ensuing brawl, Destoroyah is seemingly killed after being blown into an electrical plant. By nightfall, Godzilla and Junior meet near Haneda Airport. Their reunion is cut short when Destoroyah, having evolved and now outmatching Godzilla in height, flies in for another attack. Destoroyah knocks down Godzilla and grabs Junior, dropping him from an extreme altitude that brings the young monster close to death. Godzilla, enraged, attacks Destoroyah and a brutal battle erupts. The two creatures inflict serious wounds upon each other. Eventually, Godzilla manages to use his red spiral ray to cause damage to the floral pattern on Destoroyah’s chest, bursting it open, and a follow-up blast causes Destoroyah to spew blood from its mouth before dissolving into vapor, which later forms into the aggregate crustacean-like creatures which fought Godzilla Jr.
Godzilla tries to revive his son, but fails. Overcome by grief, Godzilla’s heart continues to fail, accelerating the meltdown. Destoroyah, having recovered from its previous injuries, appears again. Enraged, Godzilla bombards Destoroyah with a number of supercharged atomic blasts, causing tremendous damage to Destoroyah and destroying one side of Destoroyah’s head crests. Overcome, Destoroyah tries to fly away, but the JSDF shoots it down with a number of freeze weapons designed to work against Godzilla. Hitting the ground, Destoroyah disintegrates when the freezing weapons prevent it from reforming by freezing it at a molecular level.
Godzilla begins to die from the meltdown, but the JSDF is able to sustain him momentarily with the freeze weapons. Ultimately, they are unable to rescue Godzilla, and he gives one last weak roar before he melts down. While they succeeded in preventing Earth’s destruction, the JSDF has been unable to prevent the massive nuclear fallout from rendering Tokyo uninhabitable. Suddenly, the radiation levels plummet and something can be seen stirring in the mist: Godzilla Junior is apparently revived due to his father’s power being channeled into his body and he is now a full-grown adult, ready to take on his father’s title of King of the Monsters.