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, surrounding the flying saucer. With the military's attention, three holograms suddenly appeared from the craft. They were projections of the Futurians, people from the year 2204 AD. They had come to the past aboard their time machine dubbed MOTHER, the previously unidentified flying object. 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. This would release enough pollution to make Japan an uninhabitable graveyard.

The Futurians had a solution to avoid Japan's fate: remove Godzilla from history. Using a publication from Kenichiro Terasawa and Professor Mazaki, the future people believed Godzilla was born on Lagos Island. Thanks to time travel, the smaller ship KIDS aboard MOTHER was planned to carry out the history wiping.

With the help of Miki Saegusa and the two authors, the Futurians returned to Lagos Island in 1944. There they removed the "Godzillasaurus" from its home and sent it into the depths of the Bering Sea. This dinosaur they believed would eventually turn into Godzilla. By moving it, they would prevent the birth of the King of the Monsters. However, the 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. 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. An outcome the future race planed to stop. The scheme of the Futurians soon failed due to one unforeseen outcome...

Unknowingly, the Godzillasaurus in the Bering Sea was mutated due to a nuclear accident in the 1970's. The leviathan further mutated when it absorbed the energy from a nuclear sub in 1992. Seeing the obvious threat, the three-headed dragon King Ghidorah was sent to fight Godzilla. However, a raid aboard MOTHER by Kenichiro Terasawa, Emmy Kano and M-11 resulted in the time travelers' 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.