The Japanese fishing vessel Yahata Maru struggles to navigate a ferocious storm when a colossal monster emerges from an eruption on a nearby uninhabited island, launching an attack on the ship. A day later, the sole survivor, Hiroshi "Kenny" Okumura, is found by reporter Goro Maki, amidst the wreckage of the vessel.
In a bid to contain the situation, Japanese Prime Minister Mitamura is promptly informed that the creature responsible for the mayhem is none other than Godzilla. He issues an order to keep this shocking revelation hidden from the public. However, Maki's report fails to make it to publication due to concerns over "national security risks" and the potential for mass panic. Instead, he is directed to interview bio-physicist Hayashida. During his investigation, Maki encounters Naoko, Okumura's sister, serving as a lab assistant to Hayashida. Despite the government's warnings, Maki informs her that her brother is alive, prompting her to rush to the hospital.
The situation escalates when Godzilla attacks and destroys a Soviet submarine, leading the Russians to mistakenly believe that the Americans are behind it, putting international relations on the brink of war. Mitamura is briefed on the severity of the incident, including proof of Godzilla’s involvement. With the media blackout lifted, the Americans are swiftly cleared of any wrongdoing. In response, the Japanese government organizes a conference with both Soviet and American ambassadors, where Mitamura firmly establishes that nuclear weapons will not be permitted in Japanese territory, even in light of Godzilla's threats. While the Soviet representatives agree, the Americans refuse this stance. Unbeknownst to all, a Soviet Navy officer is quietly preparing a nuclear satellite, claiming a direct order from Moscow.
As Godzilla makes a sudden appearance offshore, it destroys a nuclear power plant, consuming the reactor's radiation. After briefly abandoning the reactor, Godzilla retreats, chasing a flock of birds back into the ocean. The Japan Self-Defense Forces (JSDF) are mobilized, bracing for an impending attack on Tokyo Bay. General Kakura of the JSDF presents the Japanese cabinet with details of a top-secret weapon referred to as the "Super-X attack plane," designed specifically to combat Godzilla.
Meanwhile, through the use of advanced "ultrasonic images," Hayashida discovers that Godzilla possesses a bird-like brain, albeit mutated. He realizes that Godzilla has a conditioned response to bird calls and suggests that they replicate the sounds electronically. Collaborating with the Japanese emergency task force, Hayashida proposes to lure Godzilla into Mt. Mihara's volcano using these sound frequencies. Mitamura approves both the JSDF's defense strategies and the plan to use the volcano as a trap.
In a surprising twist, Steve Martin is called in to support the Pentagon’s defense efforts against Godzilla. As the creature is sighted in Tokyo Bay, an evacuation is swiftly organized. Godzilla then launches its assault on Tokyo, prompting the JSDF to deploy the Super-X attack plane. During the chaos, Godzilla sinks a Soviet merchant vessel that is actually gathering intelligence, and in a final act, the ship’s captain launches a nuclear missile before succumbing to his injuries.
The Pentagon prepares to support their Japanese counterparts, but Martin warns that military action may only provoke further aggression from Godzilla. Hayashida, utilizing the bird signaling device, initially succeeds in calming the creature, but before further testing can occur, Godzilla is attacked anew by the JSDF. The Super-X engages Godzilla with cadmium missiles, but the tension escalates when the approaching Soviet missile is detected. With warnings that the impending blast will dwarf the Hiroshima bombing, Mitamura reluctantly permits American intervention.
As Hayashida and his signaling technology are evacuated to Mt. Mihara, the Americans successfully intercept the Soviet missile. Yet, the resulting nuclear fallout inadvertently awakens Godzilla, leading to the destruction of the Super-X. In a desperate bid to control the situation, Hayashida activates the signal once more, enticing Godzilla towards the volcano. By deploying explosives to trigger an eruption, they manage to trap Godzilla in Mt. Mihara, ending the threat that loomed over Japan.
