In 1992, Kenichiro Terasawa (Kosuke Toyohara), an author of books on psychic phenomena, learns about a group of Japanese soldiers stationed on Lagos Island in the South Pacific during World War II. The soldiers were unintentionally saved by a mysterious dinosaur known as “Godzillasaurus” which attacked and killed a group of American soldiers who had landed on the island in February 1944. While all of the Japanese soldiers on the nearby Islands fought and died in battle, the Japanese soldiers on Lagos survived the war and eventually returned to Japan. In 1954, the island was destroyed by a hydrogen bomb test and Terasawa believes that the radiation from the bomb eventually mutated the Godzillasaurus into the Godzilla which first appeared in 1984.
Yasuaki Shindo (Yoshio Tsuchiya), who commanded the Japanese soldiers on Lagos, is now a wealthy businessman who confirms the dinosaur’s existence. Meanwhile, a UFO lands on Mount Fuji. When the army investigates, they are greeted by Wilson (Chuck Wilson), Grenchko (Richard Berger), Emmy Kano (Anna Nakagawa) and android M-11 (Robert Scott Field). The visitors, known as the Futurians, explain that they’re humans from the year 2204, a time long after Japan had been completely destroyed by Godzilla. They explain that they can travel back in time to 1944 and remove the Godzillasaurus from Lagos, thereby preventing the creation of Godzilla. As proof of their story, Emmy presents to the Japanese government a copy of Terasawa’s book which hasn’t even been written yet.
Terasawa, psychic Miki Saegusa (Megumi Odaka), and Professor Mazaki (Katsuhiko Sasaki) board a time shuttle and travel back to 1944. As American forces land on the island and engage the Japanese forces commanded by Shindo, the Godzillasaurus attacks the American soldiers. However, subsequent bombardment from American naval vessels leaves it gravely wounded. After thanking the dinosaur, Shindo and his men withdraw from the island and M-11 then teleports the dinosaur to an island in the Bering Sea. The group then return to 1992, but not before the Futurians release three, small artificial creatures called Dorats on Lagos which are fused into King Ghidorah after the subsequent nuclear test in 1954. In the present, the Futurians use King Ghidorah to subjugate Japan and issue an ultimatum, but Japan refuses to surrender.
Feeling sympathy for the Japanese, Emmy reveals the truth behind the Futurians’ mission: in the future, Japan became an economic superpower that surpassed the United States, Russia, and China. The Futurians stole the time machine and plan to use King Ghidorah to alter the future by devastating present day Japan and prevent Japan’s future economic dominance over the world. After Emmy is returned to her ship by M-11, she reprograms the android. With M-11 and Terasawa’s aid, Emmy sabotages Ghidorah’s control in the UFO. However, Emmy’s companions reveal that their ship is bound to automatically return to the future in the event of sabotage, allowing them to return to a future where Japan has been destroyed either way.
Meanwhile, Shindo believes that Godzilla can be re-created using radiation from his nuclear submarine. While on its mission, however, the submarine is destroyed by Godzilla. Terasawa learns from newspaper archives that a Russian nuclear submarine sank in the 1970s near the island that Godzillasaurus was teleported to and gave off enough radiation to mutate the dinosaur into the Godzilla who attacked Tokyo in 1984.
Godzilla finally arrives in Japan and is greeted by King Ghidorah, who is sent by Wilson to destroy Godzilla. Godzilla and King Ghidorah fight at equal strength with each immune to the others attacks. Godzilla eventually ends the battle by blasting the middle head of King Ghidorah. Before the final blow, Godzilla destroys the UFO which was teleported by M-11 before it could return to the future, killing Wilson and Grenchko. Japanese troops attack Godzilla in Sapporo to no avail. Godzilla then turns his attention on Tokyo, destroying the metropolis and killing Shindo in the process.
Emmy travels to the future and returns with Mecha-King Ghidorah, a resurrected cyborg version of the original creature. Emmy relentlessly blasts Godzilla with Ghidorah’s beams, but unfortunately proved useless. Godzilla then counters by relentlessly blasting the mecha with his own atomic ray, nearly decapitating Mecha King Ghidorah. However, Emmy counters again, this time managing to knock Godzilla down. Godzilla yet proved to be too resilient, that he knocked Mecha Ghidorah down easily. Emmy had no choice, but to carry Godzilla off and drops the monster along with Ghidorah into the ocean. Emmy then returns to the future in the time shuttle but not before informing Terasawa that she is in fact a descendant of his.
At the bottom of the sea, Godzilla recovers and roars over Mecha-King Ghidorah’s remains