In 1992, the United Nations establishes the United Nations Godzilla Countermeasures Center (UNGCC) to stop Godzilla. The remains of Mecha-King Ghidorah are salvaged from the ocean and used to create two anti-Godzilla machines. The first is a flying gunship called Garuda. The second and more powerful machine, modeled after Godzilla himself, is 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 strange telepathic signal that attracts Godzilla and Rodan an adult pteranodon irradiated by the nuclear waste. Both monsters appear and fight for the egg. During their battle Godzilla critically wounds Rodan 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, just as European cuckoos leave their eggs in the nests of other birds. Godzilla appears in Japan, once again responding to the creature’s psychic call. The JSDF mobilizes Mechagodzilla, which intercepts Godzilla as he is making his way to Kyoto. The two battle, with Mechagodzilla seeming to have the upper hand, until Godzilla disables Mechagodzilla with a pulse of energy. 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 his 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, however, when Rodan, having survived his 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, attempts to escape. Super-Mechagodzilla shoots him down and Rodan lands on top of Godzilla. Rodan’s lifeforce regenerates Godzilla’s second brain and supercharges him. Now more unstoppable than before, Godzilla attacks and destroys Super-Mechagodzilla with a high-powered red 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 him to adopt Baby as his own. Baby then accepts Godzilla as his father, and Godzilla and Baby head out to the sea.