The year was 1992. The Japanese government was becoming increasingly concerned about the ever-present threat that Godzilla posed to the nation, and in response, a dynamic aerial weapon called Garuda was created in order defeat the nuclear menace. The ominous aircraft was soon rendered obsolete however, when it was replaced by Mechagodzilla, a towering mechanical beast created through research of the 23rd century technology discovered in Mecha-King Ghidorah's middle head. Though Mechagodzilla was powerful, its flaws were soon evident when it was defeated by Godzilla in their first confrontation two years later. Luckily, through the genius of Kazuma Aoki, a plan to upgrade Mechagodzilla was soon formulated. Garuda could finally be of use, for Kazuma convinced Dr. Asimov to make changes to both machines, and in a short period of time, the proper adjustments were made to form the immensely powerful fusion mech: Super Mechagodzilla!

Meanwhile, G-Force was concocting a plan by which Mechagodzilla would use the G-Crusher weapon to destroy Godzilla's secondary brain, the existence of which was confirmed during research of a recently discovered Baby Godzilla. The young creature was utilized as bait, but the mission hit a snag when the giant pterosaur, Rodan, snatched Baby's container from the transport helicopter. Pecking away at the structure, Rodan longed to reunite with the creature whom he considered a close kin. In response to this unexpected turn of events, Mechagodzilla was immediately dispatched, and Kazuma Aoki piloted Garuda closely behind...

As Garuda arrived, it became necessary to lead Rodan away from the transport container. After a short skirmish however, Garuda was hurled into a nearby building by Rodan's brute strength. As Kazuma rushed to repair his fallen vessel, Mechagodzilla's plasma grenade sent Rodan soaring into a nearby building. As soon as Rodan fell unconscious, another horror soon appeared, for Godzilla had finally arrived, determined to unite with the young Godzillasaurus. Godzilla and Mechagodzilla clashed, and the robotic reptile soon found itself crashing helplessly into the ground. Mechagodzilla was in dire straits; Garuda needed to buy it some time...

Kazuma finally made the proper repairs, and its lasers blazed! The ferocious firepower distracted Godzilla as Mechagodzilla used its thrusters to ram into its saurian foe. Godzilla was still a force to be reckoned with, and fusion was finally deemed necessary. Garuda docked onto Mechagodzilla's shoulders, and Super Mechagodzilla was born...