Three months after a volcanic eruption on Daikoku Island, the Yahata-Maru Japanese fishing vessel is caught in strong currents off its shores. As the boat drifts into shore, the island begins to erupt, and a giant monster lifts itself out of the volcano. A few days later, reporter Goro Maki is sailing in the area and finds the vessel intact but deserted. As he explores the vessel, he finds all the crew dead except for one young man called Hiroshi Okumura, who has been badly wounded. Suddenly a giant Shockirus sea louse attacks but is eventually killed with some difficulty.
In Tokyo, Okumura realizes by looking at pictures that the monster he saw was a new Godzilla. However the news of Godzilla’s return is kept secret to avoid panic until Godzilla attacks a second time and destroys a Soviet submarine. The Soviets believe the attack was done by the Americans, and a diplomatic crisis ensues, which threatens to escalate into war. The Japanese intervene and finally announce that Godzilla was behind the attack. The Japanese arrange a meeting with the Soviet and American ambassadors and, after some debate over the issue, Prime Minister Mitamura decides nuclear weapons will not be used on Godzilla even if it were to attack the Japanese mainland. The Japanese Self-Defense Forces are put on alert and search for Godzilla.
Soon, Godzilla appears on an island off the coast of Japan, determined to feed off a nuclear power plant there. When Godzilla attacks the facility and feeds off the reactor, he is distracted by a flock of birds, and leaves the facility almost as quickly as he arrived. Okumura and his friends realize that Godzilla reacts to the same signal as birds, and Professor Hayashida decides to use this method to lure Godzilla away from Tokyo. Meanwhile, the Soviets have their own plans to counter the threat posed by Godzilla, and a Soviet control ship disguised as a freighter in Tokyo Harbor prepares to launch a nuclear missile from one of their orbiting satellites should Godzilla attack.
Godzilla is later sighted at Tokyo Bay at dawn heading towards Tokyo, forcing mass evacuations out of the city throughout the day as a state of emergency is declared. Later in the evening, Godzilla abruptly appears in front of a patrol helicopter and roars as The JASDF attacks Godzilla with Mitsubishi F-1 fighter jets, but their missiles are useless against him and he shoots two of them down with his thermonuclear ray. Godzilla then proceeds to the coast, where the waiting army, equipped with tanks, rocket launchers and soldiers armed with Howa Type 64 assault rifles, proceeds to fire on Godzilla, but they are quickly subdued by a long blast of his atomic ray. At the same time, the Soviet ship hits the harbor and damages the ship and it’s circuitry, leaving the missile countdown on a timer that must be manually deactivated. The crew captain is the last member on the ship and attempts to stop the missile from launching. However, he is killed by an explosion due to an equipment malfunction. Godzilla then climbs out of the docks and proceeds towards Tokyo’s business district, wreaking havoc along the way. There, he is confronted by four laser-armed trucks known as Hyper Laser Cannons which lure him away from Professor Hayashida’s laboratory, and then the Super X, a piloted VTOL craft constructed in secret to defend Tokyo in case of emergency, in particular a nuclear attack.
Because Godzilla’s heart is similar to a nuclear reactor, the cadmium shells that are fired into his mouth by the Super X seal and slow down his heart. Unfortunately, during the fight, the city is faced with a greater threat when the countdown ends and the Soviet missile is launched from the satellite, leaving the Japanese government and people helpless to stop it. After unleashing his atomic breath on the Super X, Godzilla falls down unconscious. As the missile is predicted to hit Tokyo in 30 minutes, the Americans intervene and fire a counter missile at the Soviet missile. Professor Hayashida and Okumura are extracted from Tokyo via helicopter and taken to Mt. Mihara on Oshima island to set up the bird call device before the two missiles collide above Tokyo. The American counter missile soon hits the Russian missile and Tokyo is saved. Unfortunately, the atmospheric nuclear blast creates an electrical storm and an EMP, which revives Godzilla once more and temporarily disables the Super X.
Godzilla has a final battle with the Super X, eventually damaging the aircraft and forcing it to make an emergency landing where he destroys it by toppling a building on it. Godzilla continues his rampage, until Professor Hayashida is successful with his invention and uses the bird call device to distract him. Godzilla leaves Tokyo and swims across the Japanese sea to volcanic Mt. Mihara, where he notices the signal device. As he walks towards it, he falls into the mouth of the volcano where he is surrounded by detonators, which are activated by Okumura, creating a controlled volcanic eruption that traps Godzilla for good, at least for the time being.