In 1992, the United Nations establishes the United Nations Godzilla Countermeasures Center (UNGCC) to stop Godzilla. The remains of Mecha-King Ghidorah are salvaged and reverse engineered to create two anti-Godzilla machines, the first being an aerial gunship called Garuda and a mecha modeled after Godzilla called Mechagodzilla.
Two years later, on a mission to Adona Island in the Bering Sea, a Japanese team comes across what they assume is a large Pteranodon egg. The egg gives off a telepathic signal that attracts Godzilla and Rodan, an adult Pteranodon irradiated by the nuclear waste. Godzilla critically wounds Rodan during the ensuing battle, while the research team escapes with the egg. It's 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 in Japan, once again responding to the creature's psychic call. The JSDF mobilizes Mechagodzilla, which intercepts Godzilla as it is making its way to Kyoto. The two battle, with Mechagodzilla seeming to have the upper hand until Godzilla disables Mechagodzilla 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, Godzilla 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 a fight with Mechagodzilla. The "G-Crusher" is installed in Mechagodzilla's wrists, allowing the robot to penetrate Godzilla's hide and paralyze the monster by destroying its second brain. 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.
The UNGCC is forced to send Mechagodzilla and Garuda after Rodan instead and, in the ensuing battle, Rodan is mortally wounded. Godzilla shows up moments later and attacks Mechagodzilla. When the two appear to be evenly matched, Mechagodzilla combines with Garuda. The upgraded Mechagodzilla, called Super-Mechagodzilla, carries out the G-Crusher plan and succeeds in paralyzing Godzilla. Suddenly, the dying Rodan, once again revived by Baby's call, lands on top of Godzilla. Rodan's lifeforce regenerates Godzilla's second brain and supercharges it. Now more unstoppable than before, Godzilla attacks and destroys Super-Mechagodzilla with a high-powered red spiral atomic ray.
Godzilla finally locates Baby, who is at first afraid of the giant monster. Miki Saegusa, a young psychic woman with a link to Godzilla, telepathically communicates with Godzilla, convincing it to adopt Baby as its own. Baby then accepts Godzilla, and the two monsters head out to the sea.