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. Tsukioka lands to pickup Kobayashi and the two encounter Godzilla and a quadruped monster, who fall off a cliff into the ocean. Tsukioka and Kobayashi report to the authorities in Osaka, and find out that the quadruped is an ankylosaurus called Anguirus, whose species had an ancient rivalry with Godzilla’s species. Dr. Kyohei Yamane, who experienced Godzilla’s attack in 1954, confirms that this Godzilla is a second member of the same species, and that both monsters were likely reanimated by hydrogen bomb tests. With conventional weapons unable to kill Godzilla, Dr. Yamane suggests using flares to lure Godzilla away.

Godzilla arrives on the shore of Osaka. While a blackout of all city lights is enforced, JASDF jets use flares to lead Godzilla away from the shore. Godzilla pursues the flares, leaving the shore. Meanwhile, a prison truck transports criminals to another part of the country. The convicts hijack the truck and after a lengthy chase with the police, the truck crashes into an industrial building and starts a massive fire. The fire attracts Godzilla back to the shore. Moments later, Anguirus emerges and attacks Godzilla. As the monsters battle, the convicts attempt to escape but drown when the subway is flooded. Godzilla kills Anguirus and returns to the ocean.

Kobayashi is transferred to a Hokkaido plant. During a company party, Tsukioka and Hidemi, who came to visit, 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. Tsukioka, who has transferred to the air force, travels on a jet with an old friend. They drop bombs on Godzilla but are unsuccessful. Godzilla then wades towards shore. Kobayashi is killed while trying to distract Godzilla from returning to the ocean. Tsukioka is devastated but realizes that the military can shoot missiles at the mountain, and bury Godzilla in an avalanche. The jets fire missiles, and bury Godzilla in snow and ice.