The Japanese fishing vessel Yahata-Maru is caught in strong currents off the shores of Daikoku Island. 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 Hiroshi Okumura, who has been badly wounded. Suddenly a giant Shockirus sea louse attacks him but he is saved by Okumura.
In Tokyo, Okumura realizes by looking at pictures that the monster he saw was a new Godzilla. Maki writes an article about the account, but the news of Godzilla’s return is kept secret and his article is withheld. Maki visits Professor Hayashida, whose parents were lost in the 1954 Godzilla attack. Hayashida describes Godzilla as a living, invincible nuclear weapon able to cause mass destruction. At Hayashida’s laboratory, Maki meets Okumura’s sister, Naoko, and informs her that her brother is alive and at the police hospital.
A Soviet submarine is destroyed in the Pacific. The Soviets believe the attack was perpetrated by the Americans, and a diplomatic crisis ensues, which threatens to escalate into nuclear war. The Japanese intervene and reveal that Godzilla was behind the attacks. The Japanese cabinet meets to discuss Japan’s defense. A new weapon is revealed, the Super X, a specially-armored flying fortress that will defend the capital. The Japanese military is put on alert.
Godzilla attacks the Ihama nuclear power plant in Shizuoka Prefecture. While feeding off the reactor, he is distracted by a flock of birds and leaves the facility. Hayashida believes that Godzilla was distracted instinctively by a homing signal from the birds. Hayashida, together with geologist Minami, propose to the Japanese Cabinet, that Godzilla could be lured back to Mount Mihara on Ōshima Island by a similar signal, and a volcanic eruption could be started, capturing Godzilla.
Prime Minister Mitamura meets with Soviet and American envoys and declares that nuclear weapons will not be used on Godzilla, even if he were to attack the Japanese mainland. 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 sighted at dawn in Tokyo Bay heading towards Tokyo, causing mass evacuations. The JASDF attacks Godzilla but fails to stop his advance on the city. Godzilla soon emerges and makes short work of the JSDF stationed there. The battle causes damage to the Soviet ship and starts a missile launch countdown. The captain dies as he attempts to stop the missile from launching. Godzilla proceeds towards Shinjuku, wreaking havoc along the way. Godzilla is confronted by four laser-armed trucks and the Super X. Because Godzilla’s heart is similar to a nuclear reactor, the cadmium shells that are fired into its mouth by the Super X seal and slow down its heart, knocking Godzilla unconscious.
The countdown ends and the Soviet missile is launched, but it is destroyed by an American counter-missile. Hayashida and Okumura are extracted from Tokyo via helicopter and taken to Mt. Mihara to set up the homing device before the two missiles collide above Tokyo. The destruction of the nuclear missile produces an electrical storm and an EMP, which revives Godzilla once more and temporarily disables the Super X.
An enraged Godzilla bears down on the Super X just as it manages to get airborne again. The Super X’s weapons prove ineffective against the kaiju, resulting in even more destruction in the city as Godzilla chases it through several skyscrapers. Godzilla finally destroys the Super X by dropping a skyscraper on top of it and continues its rampage, until Hayashida uses the homing device to distract it. Godzilla leaves Tokyo and swims across Tokyo Bay, following the homing device to Mount Mihara. There, Godzilla follows the device and falls into the mouth of the volcano. Okumura activates detonators at the volcano, creating a controlled eruption that traps Godzilla inside.