After the UNGCC (United Nations Godzilla Countermeasure Center) concluded that the super military jet Garuda was ineffective against Godzilla, the bionic technology recovered from Mecha-King Ghidorah's severed neck was adapted to form Godzilla's robotic doppelganger: Mechagodzilla! Reinforced with an artificial diamond coating and a wide variety of offensive weaponry, this machine would assist the world in combating Godzilla's ever-present threat.

In 1994, Mechagodzilla's first mission was to repel Godzilla, who had come ashore to locate Baby Godzilla. The mechanical clone flew into the sky and landed to face its organic counterpart. It's mega-buster ray, eye lasers, paralysis missiles, and plasma grenade bombarded and overwhelmed the monster. Mechagodzilla's shock anchors and cables were fired, and it appeared as though the king of the monsters had finally met its superior. Alas, the energy surged back into Mechagodzilla and the once technological wonder was left immobile on the dusty terrain.

Mechagodzilla was not out of commission, however. A new plan of attack was concocted, and Baby Godzilla was used as bait. Rodan interrupted the plan, and Mechagodzilla arrived for its second mission, accompanied by Garuda. Garuda was quickly subdued by the terrible pterosaur, but Mechagodzilla's mega-buster and plasma grenade quickly repelled and seemingly defeated Rodan.

As Rodan fell into unconsciousness, Godzilla suddenly arrived. Mechagodzilla and Godzilla's beams clashed, and Mechagodzilla overheated. Godzilla began to land physical blows against the machine, and it quickly gained the upper hand. A repaired Garuda began to grapple with Godzilla, as Mechagodzilla recovered and returned to the fray. In order to assist Mechagodzilla, Garuda proceeded to dock with the host robot, and a new mech was born.

If not for the combined genius of Kazuma Aoki and Dr. Asimov, the amalgamated mech known as Super Mechagodzilla would never have come into being. The combination of both Mechagodzilla and Garuda would undoubtedly increase the odds of winning against Godzilla, and in the middle of battle, the two mechs merged for the first time.

Super Mechagodzilla fought Godzilla in a show of raw power, releasing its full arsenal on the once terrible tyrant. The ultimate anti-Godzilla weapon, the G-Crusher, was readied. Using the psychic prowess of Miki Saegusa, Godzilla's secondary brain was located and the G-Crusher was fired directly into it! The brain was ruptured and the creature was left completely paralyzed.

Rodan suddenly awoke, responding to Baby Godzilla's cries. It began to fly into the sky, but Super Mechagodzilla gave it no opportunity to fight. Rodan was shot down, and it landed atop the paralyzed Godzilla. It gave its life and revived Godzilla with all of its energy. Godzilla's power increased greatly, and it utilized its new spiral ray to knock Super Mechagodzilla out of commission. The crew survived, but Mechagodzilla was no more.

As Mechagodzilla lay ruined, humankind could only watch helplessly as Godzilla and Baby Godzilla returned to the sea.