Tsukioka works for the Kio Cannery near Osaka as a scout plane pilot - sighting schools of tuna from the air and radioing the position back to headquarters, which in turn alerts the fishing fleet. Tsukioka discovers such a school and reports back to his sweetheart Hidemi, who works in the cannery's radio room.

At the same time, Tsukioka's friend Kobayashi is also out scouting. He reports engine trouble and has to land near Iwato Island. Hidemi radios Tsukioka and the pilot decides to try and find his friend. After circling the barren Iwato Island, he sights the plane ditched on the beach. Nearby is Kobayashi, waving up at him. Tsukioka lands and joins his friend on the craggy shore to await the arrival of a ship to retrieve Kobayashi's plane.

Suddenly, terrible roars terrify the two men. Above them on the cliffs, two horrible monsters are locked in battle. The pilots retreat into a crevice to avoid the rain of rubble the brutes' fight causes. At last, they make a run for Tsukioka's plane and escape. The monsters fight on, at last toppling into the sea.

Back in Osaka, Tsukioka and Kobayashi report to the authorities. A conference is quickly called between Japan's head scientists and military commanders. Kobayashi identifies one monster as an Anguirus. The other monster is another Godzilla, dubbed Gigantis. The Anguirus, Dr. Tadokoro says, were murderous brutes from prehistoric times, quoting a book titled Anguillasarus, Killer of the Living. Dr. Yamane takes over the discussion, saying that there is no weapon that can kill Gigantis. He shows a film to the assembly. First there is a scientific recreation of Earth's prehistory and the theoretical fire creatures that thrived in the molten past. These creatures retreated underground when the earth cooled. Radiation revived these creatures. Dr. Yamane then shows footage of Godzilla's attack on Tokyo. The oxygen destroyer used to kill Godzilla cannot be recreated, as its designer is also dead. And, of course, the big problem is that this time there are two monsters. He suggests that fire attracts and enrages these creatures and that flares might be used to draw the monsters away from the cities.

Tsukioka and Hidemi enjoy a quiet moment on the roof of the cannery. Tsukioka questions his own bravery, ignoring Hidemi's light-hearted assurances. The sudden appearance overhead of a formation of jets interrupts the lovers. At defense headquarters news is gathered regarding the hunt for Gigantis and Anguirus. Cruisers, planes and even subs hunt the monsters at sea while radar units keep watch on land. Gigantis is sighted near Osaka but it is soon speculated that he may bypass the city. The news causes Osaka to erupt into celebration. Tsukioka and Hidemi dance in their favorite nightclub when the alarm sounds. Gigantis has been sighted again, this time approaching Osaka. Tsukioka drives Hidemi out of the city to her father's house in Kio. There Kobayashi gives him the news that Hidemi's father, their boss, has gone to the cannery. Tsukioka and Kobayashi drive back to Osaka to try and talk Kohei Yamaji into leaving the city.

Meanwhile, tanks and cannons take position on the waterfront. Gigantis is spotted in the harbor, drawing nearer the city. Jets fly overhead, dropping flares to distract the beast. Evacuation of Osaka is ordered and the citizens begin to flee into the hills. The flares finally work, luring Gigantis away and back out to sea.

All the same, the authorities are taking no chances and the prisons are evacuated. Inside one prison truck, a group of hard-cases plans to escape in the confusion. They manage to overcome their guards and escape from the truck. Some of the men are immediately recaptured, but the others split up, police running after one group. The band being chased seizes an abandoned fuel truck and drives off in it. At that moment, Tsukioka and Kobayashi's car appears and is stopped by the police. They are soon told to give chase to the truck. The convicts are pursued by the police into Osaka's industrial are. They loose control of the truck and crash into an oil refinery. The resulting explosion ignites the oil, causing a huge fire. Out at sea, Gigantis sees the fire. Ignoring the flares, he turns and heads back toward Osaka.

As Gigantis advances on the city, the military attacks. Tanks, cannons, rockets and bombs are all useless. Gigantis bathes his attackers in fiery breath and begins to destroy Osaka. Soon, also drawn by the fire, Anguirus arrives. The two monsters resume their battle and the JSDF scrambles to get out of their way. Gigantis' breath ignites whole city blocks. At the cannery, Tsukioka finally convinces Kohei Yamaji to abandon his building and leave the city when the battle reaches his nearby factory.

Gigantis and Anguirus continue to batter each other with fang and claw. The struggle even reaches the last of the escaped convicts, who flee into Osaka's subway to escape the beasts. But their reprieve is short, for the monsters cause a retaining wall to collapse, flooding the tunnels with seawater. Even defense headquarters is forced to evacuate. Soon, the monsters are fighting within the walls of Osaka Castle, destroying the ancient fortress. Gigantis finally bests Anguirus, ravaging Anguirus' throat with his fangs and incinerating the dying monster with a blast of radioactive flame. Osaka burns as the victorious Gigantis returns to the sea.

In the ruins, Kohei Yamaji announces that he will rebuild. Branch foreman Shibeki joins Yamaji in surveying the damage. For the time being, the Osaka ships will join those in Hokkaido. Yamaji also decides to send Kobayashi to Hokkaido as well.

Business is back to normal, Kobayashi sighting fish for Shibeki's ships. The catch is greatly anticipated. Kobayashi is surprised to hear Tsukioka and Hidemi at the other end of the radio. When he lands, Kobayashi takes his two friends to an inn, where Tsukioka is reunited with Tajima, an old air corps comrade. They are soon invited to join Tsukioka's old commander Terazawa and his squadron for a party. The festivities are interrupted when Mr. Shibeki arrives. Gigantis has attacked the fleet. Kohei Yamaji confirms the information for Terazawa, who immediately orders his men to scramble their fighters and find the monster. News of Gigantis' return spreads across the Pacific, plunging the world into panic. Coastal cities in Japan are evacuated. Even civilian planes are pressed into the hunt. Tsukioka patrols the icy sea north of Hokkaido, trying to sight Gigantis, bravely continuing even in stormy weather.

In Hokkaido, Kobayashi meekly asks Hidemi what sort of gift he might buy for his own girl. The conversation is cut short when Tsukioka radios that he has spotted Gigantis. Kobayashi at once heads for his plane, to relieve Tsukioka before his plane runs out of fuel. Gigantis emerges on the icy shore of Kawito Island. Kobayashi takes over the watch and Tsukioka returns to Hokkaido. He leads Tajima's squadron back to the island, explaining the situation at the island to Commander Terazawa. Landing craft are also sent out to block the narrow mouth of the canyon Gigantis has entered.

Kobayashi tries to keep Gigantis in the canyon by buzzing the monster in his plane. The air corps jets arrive, bombing Gigantis. The attack is unsuccessful, and Gigantis is still headed toward the beach. Kobayashi again buzzes Gigantis, but Gigantis' fire cripples the plane. Kobayashi crashes into the icy canyon wall, starting an ice slide. Tsukioka sees Kobayashi's death and realizes that his friend has shown them how to destroy Gigantis. The jets seize upon Tsukioka's idea, to start an avalanche and bury Gigantis. The jets do not have enough firepower to finish the job, however, and return to base.

Tsukioka begs Tajima for a jet, wishing to get revenge on Gigantis for Kobayashi's death. Back at Kawito Island, Gigantis begins to dig his way from the ice. The landing craft arrive and troops block the canyon mouth with oil drums. They escape as Gigantis advances. Machine-gun fire ignites the oil and Gigantis shies away from the wall of flame. Heading back into the canyon, Gigantis is soon attacked by a second, larger force of jet fighters.

The jets launch missiles into the canyon walls. Although some are brought down by Gigantis' fire, enough succeed in the attack to start several avalanches of ice. Gigantis is completely buried beneath the ice and snow, entombed forever. Tsukioka circles the icy grave and silently mourns his friend Kobayashi.