In 1991, following the events of Godzilla vs. King Ghidorah, the United Nations establishes the United Nations Godzilla Countermeasures Center (UNGCC) to stop Godzilla. Their military branch, G-Force, salvages Mecha-King Ghidorah’s remains and use them to reverse engineer two anti-Godzilla machines: an aerial gunship called Garuda and a mecha modeled after Godzilla called Mechagodzilla.

Two years later, while on a mission to Adona Island, a Japanese team comes across what they assume is a large Pteranodon egg, which gives off a telepathic signal that attracts Godzilla and Rodan, an adult Pteranodon irradiated by nuclear waste. Godzilla critically wounds Rodan during the ensuing battle while the research team escapes with the egg. It is taken to a research center in Kyoto, where it imprints on a young female scientist. When a Baby Godzilla hatches from the egg, the research team concludes that the egg was left in the Pteranodon nest with Rodan in a manner similar to the brood parasitism displayed by European cuckoos. Godzilla appears, once again responding to the creature’s psychic call. The JSDF mobilizes Mechagodzilla, which intercepts Godzilla as it is heading to Kyoto. The two battle, with Mechagodzilla initially having the upper hand until Godzilla disables the robot with an energy pulse. Godzilla continues searching for Baby, but the scientists, having discovered the telepathic link between the monsters, shield it from Godzilla. Frustrated, it destroys most of Kyoto before returning to the ocean.

Tests on the baby reveal that it has a second brain in its hips that controls the animal’s movement. The UNGCC assumes that this also holds true for Godzilla, and decide to use Baby to bait Godzilla into another fight with Mechagodzilla. The “G-Crusher” is installed into Mechagodzilla, which will allow the robot to penetrate Godzilla’s hide and destroy its second brain. Young psychic Miki Saegusa is ordered to become a part of Mechagodzilla’s crew to locate Godzilla’s second brain. While she is reluctant due to her mental connection with Godzilla, she agrees. The plan backfires when Rodan, having survived its battle with Godzilla and further mutated by radiation, responds to Baby’s call and intercepts the UNGCC transport.

In response, they send Mechagodzilla and Garuda after Rodan instead, which mortally wound it. Godzilla arrives soon after and attacks Mechagodzilla. The fight is evenly matched until Mechagodzilla combines with Garuda to become Super-Mechagodzilla and use the G-Crusher to successfully paralyze Godzilla. Suddenly, the dying Rodan, revived by Baby’s call, begins flying towards it, but is shot down by Super-Mechagodzilla, crashing atop Godzilla. Rodan’s life force regenerates Godzilla’s second brain and supercharges the monster. Now more powerful than before, Godzilla attacks and destroys Super-Mechagodzilla with a high-powered, spiral-shaped atomic ray.

Godzilla locates Baby, who is initially afraid of the giant. Miki telepathically communicates with Baby, convincing it to go with Godzilla. The two monsters head out to the sea.