Within a year Godzilla is back at the cinema and it begins with two pilots named Shoichi Tsukioka and Koji Kobayashi are hunting for schools of fish for a tuna cannery company in Osaka. Kobayashi’s plane malfunctions and is forced to land near Iwato Island, an uninhabited strip of rocks formed by volcanic eruptions. Tsukioka then looks for Kobayashi and finds him safe, with only a wrist sprain. While talking, the two men hear some strange sounds and find two monsters fighting. Tsukioka immediately recognizes one of the monsters to be Godzilla. The two monsters then fall off a cliff, into the ocean.
Tsukioka and Kobayashi report to the authorities in Osaka, and find out that the other monster Godzilla was fighting is Anguirus. A group of scientists with the two pilots research Anguirus in a book written by a Polish scientist. Godzilla and Anguirus lived around the same time millions of years ago, and there was an intense rivalry between the two monsters.
Archaeologist Kyohei Yamane, who experienced Godzilla’s attack in 1954, is also present at the meeting, and shows a film (composed of clips from the 1954 film) of the original Godzilla attacking Tokyo. He confirms that this Godzilla is a second member of the same species, and that it and Anguirus were probably brought back to life by the same hydrogen bomb tests that awoke the original Godzilla. Yamane states that there is no way to kill Godzilla, and that Daisuke Serizawa, the inventor of the Oxygen Destroyer, had died and burned the formula. Yamane, though, suggests that the military should use flares on Godzilla to attract the monster away from the shore as Godzilla becomes angry when it sees lights because the hydrogen bomb’s bright explosion had awakened and mutated it.
Godzilla arrives on the shore of Osaka. While a blackout of all city lights is enforced, JASDF jets are sent to shoot flares from their planes to lead Godzilla away from the shore. Godzilla sees the flames, and, as Yamane predicted, starts to leave.
Meanwhile, a prison truck transports dangerous criminals to another part of the country. All of the criminals, using body language, convey to each other that the cover of darkness caused by the city’s blackout provides a great opportunity to escape from prison. The prisoners beat up the two policemen guarding them inside the truck, and run away. A few of them find a gasoline truck, and use it to escape. The truck crashes into an industrial building and starts a massive fire.
The fire, much brighter than the planes’ flares, attracts Godzilla back to the shore of Osaka. A few minutes later, Anguirus swims to shore and attacks Godzilla. The two creatures fight an intense battle, while destroying several buildings, including the tuna cannery that Tsukioka and Kobayashi work for. In the course of the battle, the criminals are drowned in the subway when it is flooded by the thrashing of the two monsters. Godzilla finally bites Anguirus’s neck, and throws it upside down into a moat near Osaka Castle. Godzilla then fires its atomic ray at Anguirus, burning it to death in the ruins of the famed castle.
Tsukioka and Kobayashi are transferred to a Hokkaido plant. During a company party, Tsukioka and Kobayashi are notified that Godzilla destroyed one of the company fishing boats. The military and Tsukioka begin a massive search for Godzilla. Tsukioka spots Godzilla swimming to the shore of a small, icy island. He notifies the cannery, and Kobayashi takes off in his plane to switch shifts with Tsukioka.
Kobayashi dives his plane towards Godzilla to distract it from walking back into the ocean. Tsukioka, who has transferred to the air force, travels on a jet with an old college friend. They drop bombs on Godzilla but are unsuccessful. Godzilla then wades towards shore. Kobayashi dives towards Godzilla again but Godzilla fires its atomic ray on Kobayashi’s plane. The plane then crashes on an icy mountain, killing Kobayashi.
Tsukioka is devastated but realizes that the military can shoot missiles at the mountain, and bury Godzilla in an avalanche, thereby freezing it to death. The jets fire their missiles, and bury Godzilla in snow and ice up to its mid-section.
The jets return to base to reload, and Tsukioka is authorized to fly in his own jet. The jets return to the icy island, only to find that Godzilla is digging its way out of the previous avalanche. They fire a fresh round of missiles at the mountain, triggering a new avalanche, burying Godzilla up to its neck. Tsukioka then fires his own missiles, burying Godzilla completely, thereby finishing the job. The men return home and receive the homage of a grateful nation, and Tsukioka and the woman he loves are at last able to go forward with their lives in peace.