Reports of an unidentified flying object caught the public's attention across the whole of Japan during the summer of 1992. The mystery thickened when two scout helicopters suddenly disappeared in the area where it was determined that the UFO had landed. The self-defense force was dispatched, and as the flying saucer was surrounded, three holograms suddenly appeared. They were projections of the Futurians, people from the year 2204 AD, who had come to the past aboard their time machine dubbed MOTHER. They arrived to submit a grave warning to Japan about a dreadful future. They foretold of a time when Godzilla would destroy a portion of the nation's nuclear reactors, effectively releasing enough pollution to make Japan an uninhabitable graveyard.

With the help of Miki Saegusa, Kenichiro Terasawa, and Professor Mazaki, the Futurians returned to 1944 and removed the "Godzillasaurus" from its home on Lagos Island and sent it into the depths of the Bering Sea, for this was the dinosaur that would eventually mutate into Godzilla! The sinister, duplicitous Futurians left three genetically engineered pets, the Dorats, in the dinosaur's place. The three golden imps mutated and merged due to the nuclear tests that occurred a decade later, and the resulting amalgam, King Ghidorah, was sent to destroy Japan by the Futurians in the present day. What were the motives of the Futurians? In truth, the time travelers were attempting to halt Japan's economic advancement. By the 23rd century, Japan would become the most economically powerful nation on the planet, dwarfing every other country on Earth! The plans of the Futurians soon failed, however.

The Godzillasaurus in the Bering Sea was unknowingly mutated due to a nuclear accident in the 1970's, and the leviathan further mutated when it absorbed the energy from a nuclear sub in 1992. The three-headed dragon, King Ghidorah, was sent to fight Godzilla, but a raid aboard MOTHER by Kenichiro Terasawa, Emmy Kano and M-11 resulted in the time travellers' losing control over the hateful hydra. Godzilla quickly gained the upper hand shortly thereafter. As MOTHER was attempting to escape and return to the 23rd century, M-11 teleported the flying saucer to Godzilla's position. Before the ruthless reptile prepared to annihilate King Ghidorah, it blasted MOTHER with its thermonuclear heat ray. The evil Futurians were finally defeated, and their plot to destroy Japan was thwarted!