In 1984, the Japanese fishing vessel Yahata Maru is swept by strong currents off the shores of Daikoku Island as the island begins to erupt, and a giant monster lifts itself from 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 ship, he discovers the crew dead except for Hiroshi Okumura, who has been badly wounded. A giant Shockirus sea louse attacks him, but he is saved by Okumura.
In Tokyo, Okumura realizes by looking at pictures that the monster is Godzilla. Maki writes an article about the account, but the news of Godzilla’s return is kept secret and his piece is withheld. Maki then visits Professor Makoto 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 Naoko Okumura, and he's the one who 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 carried out by the Americans, and a diplomatic crisis escalates toward nuclear war. The Japanese intervene and reveal that Godzilla was behind the attacks. The Japanese cabinet meets to discuss Japan’s defense, and a new weapon is revealed: the Super X, a specially armored flying fortress designed to defend the capital. The Japanese military is put on alert.
Godzilla attacks the Mihama nuclear power plant in Shizuoka Prefecture. While feeding off the reactor, it is distracted by a flock of birds and leaves the facility. Hayashida, together with geologist Professor Minami, proposes that Godzilla could be lured back to Mount Mihara on Ōshima Island by a similar homing signal, so a volcanic eruption could trap the creature.
Prime Minister Seiki Mitamura meets with Soviet and American envoys and declares that nuclear weapons will not be used on Godzilla, even if Godzilla were to attack the Japanese mainland. Meanwhile, the Soviets have their own plan: 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 toward Tokyo, causing mass evacuations. The JASDF attacks Godzilla but fails to stop its advance on the city. Godzilla finally emerges and devastates the area around Shinjuku. The battle draws damage to the Soviet ship and triggers a missile countdown. The captain dies as he attempts to stop the launch. Godzilla proceeds through Tokyo, chased by four laser-armed trucks and the Super X. Because Godzilla’s heart is similar to a nuclear reactor, the cadmium shells fired into its mouth slow and temporarily knock out its heart.
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 by 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 creates an electrical storm and an EMP, reviving Godzilla and temporarily disabling 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, causing more destruction in the city as Godzilla chases it through several skyscrapers. Godzilla finally destroys the Super X by dropping a skyscraper onto it. Godzilla 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.
