Time travelers from 23rd century, or "Futurians", returned to the Earth's past to prevent the Godzillasaurus on Lagos Island from eventually mutating into Godzilla. The dinosaur was teleported to the bottom of the Bering Sea, and in his place, they left three genetically engineered pets that would eventually merge and mutate into the ultimate super weapon: King Ghidorah. It was the Futurians' plan to decimate Japan in the year 1992, decades before the nation would ultimately become a corrupt superpower. King Ghidorah, their remotely controlled monster, would be their tool for Japan's annihilation!

The organic weapon of mass destruction was unleashed on Kyushu. King Ghidorah grazed Fukuoka Tower and descended amongst the buildings of Kyushu's largest city. The three-headed demon exhaled its gravity beams, which caused massive explosions and citywide damage. After King Ghidorah was finished in Kyushu, it began to fly to Hokkaido, where it would cause even more damage!

In order to counter this threat, the government decided to use nuclear weaponry to mutate the dinosaur lying at the bottom of the Bering Sea. When they released a secret nuclear submarine to mutate the Godzillasaurus, little did they realize that the dinosaur had already undergone irradiation some years earlier. Godzilla was already born, and as the nuclear sub approached, the towering titan destroyed it! The resulting radiation mutated the creature to an even greater extent, and Godzilla now stood at an incomprehensible 100 meters in height. The unstoppable monster began to move toward the mainland...

After King Ghidorah engaged in a brief aerial battle with the Japanese Self-Defense Force, it landed to meet Godzilla face-to-face. After a brief exchange of their energy beams, King Ghidorah took to the sky. Circling around its opponent, King Ghidorah fired its gravity beams on Godzilla, who countered with his thermonuclear ray. The dreadful dragon slammed into its foe, and King Ghidorah began to crush Godzilla with its feet. Suddenly the Futurians lost control of their ultimate weapon! Godzilla was quick to take advantage of this situation, and the merciless monster grabbed the two squirming tails of his confused enemy. Godzilla lifted his foe into the air and slammed it into the ground. This savage attack continued, and King Ghidorah was thrown aside. The detestable dragon rose once more and clamped onto Godzilla with his outer heads. Its middle head coiled around the neck of the colossus, and Godzilla began to foam at the mouth. Godzilla released his nuclear pulse and fired his thermonuclear ray. The horrible hydra's middle head flung into the air! As the maimed monster attempted to escape into the sky, Godzilla bore a hole through its left wing. King Ghidorah plummeted into the sea, where it was left undisturbed for over two centuries...

Meanwhile, the newly revamped Godzilla began to march its way through the mainland. One terror was defeated, but another had just begun its terrible onslaught!

Upon defeating King Ghidorah and sending the brass behemoth to its doom in the depths of the sea, Godzilla began to wreck havoc throughout Japan. Emmy Kano, a Futurian who rebelled against her belligerent crew, was asked if King Ghidorah could be revived in the 23rd century. If possible, it could be brought back to the present and used as an anti-Godzilla weapon to protect Japan. Emmy agreed with this request and ventured into the future using the time machine KIDS.

As Godzilla continued his rampage through the center of Tokyo, he suddenly heard a sound in the sky. King Ghidorah, now the cyborg Mecha-King Ghidorah, materialized in a flash of pulsing energy. Piloted by Emmy and reinforced with several robotic segments, Mecha-King Ghidorah easily outclassed its predecessor. It fired its gravity beams and triple laser beam at its foe. Though Godzilla managed to fire his thermonuclear breath in retaliation, the gray gargantuan was ultimately sent crashing into the surrounding buildings. Godzilla managed to regain his balance and damage both of Mecha-King Ghidorah's wings. It was time for Emmy to reveal the cyclopean cyborg's most powerful technique. Energy-conducting capture cables were fired, as was the machine hand restraint. Mecha-King Ghidorah lifted Godzilla into the sky and over the sea, but both were sent crashing into the waves when Godzilla fired his thermonuclear ray at his captor. Emmy quickly escaped in KIDS, leaving both monsters trapped on the ocean floor.

Meanwhile, beneath the surface of the sea, Godzilla's eyes glowed eerily. It released its thermonuclear ray into the azure abyss, for it would escape from it restraints and return to terrorize the world another day...