In 1992, science fiction writer Kenichiro Terasawa (Kosuke Toyohara) is writing a book about Godzilla and learns of a group of Japanese soldiers stationed on Lagos Island during the Gilbert and Marshall Islands campaign. In February 1944, while threatened by American soldiers, the Japanese soldiers were saved by a mysterious dinosaur. He theorizes that the dinosaur was subsequently mutated into Godzilla in 1954 after a hydrogen bomb test on the island. Yasuaki Shindo (Yoshio Tsuchiya), a wealthy businessman who commanded the Japanese soldiers on Lagos Island, confirms that the dinosaur did indeed exist.
Meanwhile, a UFO lands on Mount Fuji. When the Japanese army investigates, they are greeted by Wilson (Chuck Wilson), Grenchko (Richard Berger), Emmy Kano (Anna Nakagawa) and an android, M-11 (Robert Scott Field). The visitors, known as the "Futurians", explain that they are humans from the year 2204, where Godzilla has completely destroyed Japan. The Futurians plan to travel back in time to 1944 to remove the dinosaur from Lagos Island before the island is destroyed, thus preventing the mutation of the creature into Godzilla. As proof of their story, Emmy presents a copy of Terasawa's book, which has not yet been completed in the present.
The Futurians, Terasawa, Miki Saegusa (Megumi Odaka), and Professor Mazaki (Katsuhiko Sasaki), board a time shuttle and travel back to 1944 to Lagos Island. There, as American forces land and engage the Japanese forces commanded by Shindo, the dinosaur attacks and kills the American soldiers. The American navy then bombs the dinosaur from the sea and it is gravely wounded.
After Shindo and his men leave the island, M-11 teleports the dinosaur from Lagos Island to a place in the Bering Strait. Before returning to 1992, the Futurians leave three small creatures called Dorats on Lagos Island, which are exposed to radiation from the hydrogen bomb test in 1954. The creatures merge to become King Ghidorah, which then appears in present-day Japan. After returning to 1992, the Futurians use King Ghidorah to subjugate Japan. They issue an ultimatum, but Japan refuses to surrender.
Feeling sympathy for the Japanese people, Emmy reveals to Terasawa the truth behind the Futurians' mission: in the future, Japan is an economic superpower that has surpassed the United States, Russia, and China. The Futurians traveled back in time in order to change history and prevent Japan's future economic dominance by creating King Ghidorah and using it to destroy present day Japan. At the same time, they also planned to erase Godzilla from history so it wouldn't pose a threat to their plans. After M-11 brings Emmy back to the UFO, she reprograms the android so it will help her. With M-11 and Terasawa's aid, Emmy sabotages the UFO's control over King Ghidorah.
At the same time, Shindo plans to use his nuclear submarine to recreate Godzilla. On route to the Bering Strait, Shindo's submarine is destroyed by an already mutated Godzilla, who absorbs its radiation and becomes even larger and more powerful. Terasawa discovers that a Russian nuclear submarine sank in the Bering Strait in the 1970s. The Russian submarine released enough radiation to mutate the dinosaur into Godzilla, effectively setting in motion the events of The Return of Godzilla onwards.
Godzilla arrives in Japan and is met by King Ghidorah. They fight at equal strength, each immune to the other's attacks. Godzilla eventually ends the battle by blasting off Ghidorah's middle head. Before the final blow, Godzilla destroys the UFO, killing Wilson and Grenchko. Godzilla then turns its attention on Tokyo, destroying the metropolis and killing Shindo.
Emmy travels to the future with M-11 and then returns to the present day with Mecha-King Ghidorah, a cybernetic version of King Ghidorah. The cybernetic Ghidorah blasts Godzilla with energy beams, which proves useless. Godzilla then counters by relentlessly blasting Ghidorah with its atomic ray, almost decapitating Ghidorah. Ghidorah survives but then Godzilla prevails, knocking Ghidorah down. Emmy carries off Godzilla and drops it and Ghidorah into the ocean. Emmy then returns to the future but not before informing Terasawa that she is his descendant.