The Japanese fishing vessel Yahata Maru is trying to find its way to shore in a horrible storm, when a giant monster emerges from an eruption on a nearby uninhabited island and attacks the boat. A day later, reporter Goro Maki finds the vessel intact, along with its sole survivor Hiroshi "Kenny" Okumura.

The Japanese Prime Minister, Mitamura, is informed of the attack and that the monster is Godzilla; he orders that this be kept secret from the public. Maki's report is not published by his newspaper because it is "national security risk” and could cause mass panic. Maki is told to interview bio-physicist Hayashida instead. Maki finds Naoko, Okamura's sister working as a lab assistant to Hayashida and informs her that her brother is safe, against the government's orders. She rushes to the hospital.

Godzilla attacks and destroys a Soviet submarine. The Russians believe the attack was orchestrated by the Americans and the situation threatens to escalate into war. Mitamura is informed of the submarine attack and shown evidence that Godzilla was responsible. The media blackout is lifted and the Americans are absolved of blame. The Japanese arrange a meeting with the Soviet and American ambassadors. Prime Minister Mitamura decides nuclear weapons will not be allowed in Japanese territory even if Godzilla were to attack the Japanese mainland. The Americans balk at this, while the Soviets are in full agreement. However, a Soviet Navy officer secretly prepares a nuclear satellite, claiming Moscow has ordered this.

Godzilla appears on an island off the coast of Japan and attacks a nuclear power plant, removing the nuclear reactor and feeding off the radiation. Godzilla suddenly drops the reactor and follows a flock of birds back out to sea. The Japan Self-Defense Forces are deployed to wait for a possible attack by Godzilla at Tokyo Bay. General Kakura of the JSDF briefs the Japanese cabinet about a top-secret weapon known as the "Super-X attack plane" that can be used against Godzilla.

Through the use of "ultrasonic images", Hayashida determines that Godzilla's brain is bird-like, only mutated. Hayashida realizes that Godzilla has a conditioned response to birds chirping and suggests they duplicate the sound electronically. Hayashida assists the Japanese emergency task force and plans to lure Godzilla into Mt. Mihara's volcano by emitting bird sound frequencies. The Prime Minister authorizes both the JSDF plan and the plan to use the volcano against Godzilla.

Steve Martin is brought into the Pentagon to assist against Godzilla. Godzilla is sighted in Tokyo Bay, which is immediately evacuated. Godzilla proceeds to attack Tokyo and the JSDF launch the Super-X. In the attack, Godzilla sinks a Soviet merchant ship which was in actuality an intelligence collection vessel. Before dying of his injuries, the captain launches the nuclear missile.

The Pentagon prepares to assist the Japanese but Martin cautions that weapons will only confuse and antagonize Godzilla further. Hayashida uses the bird signaling device on Godzilla, which works initially, but before it can be tested further, Godzilla is attacked again by the JSDF. The Super-X arrives and defeats Godzilla with cadmium missiles. At that moment, the Soviet missile is detected by the Americans as it draws closer to Japan. When Washington warns that the blast will be 50 times that of the Hiroshima bombing Mitamura permits the Americans to make an interception attempt.

Hayashida and his signaling equipment are evacuated and sent to Mt. Mihara. The Americans launch a counter-missile and successfully intercept the Soviet missile. However, the nuclear blast fallout reawakens Godzilla and it destroys the Super-X. Hayashida relaunches the signal and lures Godzilla into the mouth of Mt. Mihara. Using explosive bombs to cause the mountain to erupt, Godzilla becomes imprisoned after falling into the volcano.