In a seaplane searching for tuna pilot, Tsukioka (Hiroshi Koizumi) appears to spot a school before circling a ship, and reporting his position to base. Hidemi (Setsuko Wakayama), the base radio operator flirts briefly with him, then makes arrangements for a date.
Another seaplane develops engine trouble near the southern Islands, pilot Kobayashi (Minoru Chiakai) reports that he is going down for a crash landing. Hidemi contacts Tsukioka and orders him to begin searching for Kobayashi. Flying low over an island Tsukiokai sees Kobayashis plane intact on a beach and lands to investigate. Finding Kobayashi is uninjured they make plans to leave the island, the discussion is interrupted by a strange roaring noise followed by a huge creatures head poking between rock outcrops.
Fleeing the scene, the men hide behind some rocks and watch the creature. Godzilla says Tsukioka. Continuing to watch, it becomes apparent that Godzilla is fighting another similar sized creature. During the battle, both animals slip and disappear into the ocean.
Back in Osaka, the men a questioned about what they saw. The second creature is identified as an angilosaurs or angilas. This is the realization of Professor Yamanes (Takashu Shimura) greatest fear; he always believed that Godzilla was not a one of a kid creature, now he has evidence. It is known that Angilas was a clever creature with a great hatred of predatory animals, and the resumption of this hatred is what the pilots witnessed
Yamane then shows a series of films from Godzillas attack a few years before, and admits since the scientist who invented the oxygen destroyer is dead, they have no solutions for how to deal with the monster.
Yamane then explains his theory that a second Godzilla with Angilas emerged because of a recent round of atomic tests. He recalls the original Godzilla was affected by bright emergency lights and seemed to make him angry. Yamane proposes that if the creature comes ashore in Tokyo to drop light bombs in front of the creature to lure it away.
Overnight the Japanese air force search for Godzilla, it is not till the next morning that word is received that plane 54 has a radar contact on the creature, then frigate T-10 picks up the same contact. A plane is dispatched to follow the creature and it appears Godzilla is staying out to sea.
The Japanes 4th fleet is dispatched to surround the creature and attempt to engage him while he is still away from the coast. In Osaka life goes on, Tsukioda and Hidemi attend a dance when the music is interrupted. Godzilla has changed course and is expected to make landfall near Osaka. The population is asked to head for shelters and all the city lights are to be turned off so Yamane can test his light bomb.
The Japanese air force begin their attack as various tanks and other equipment deploys along the coast to repel the attack. Godzilla is sighted and the light bombs are dropped. Godzilla reacts with confusion and begins to move back out to sea. The authorities relax a little, thinking the plan has worked
Elsewhere a prison truck with a load of convicts is traveling down the darkened roads. One of the guards is attacked and the driver forced to stop the vehicle. Once the truck is stopped the prisoners stage a mass break out scattering quickly.
Three convicts commandeer a tanker truck and are chased by two police who have taken a car being driven by Tsukioka and Kobayashi. The chase leads into an oil refinery, where the vehicle fails to stop in time. As a result of the accident flames leap high into the sky attracting the attention of Godzilla.
As the fire intensifies Godzilla turns back towards Osaka, both the army and air force attack. Suddenly from the other side of the bay Angilas appears. The second creature moves in and begins fighting Godzilla
Large sections of Osakas docklands are in flames as the two creatures continue to battle. Hidemi, safely away from the city fears the worst knowing that Tsukioka was near the area helping her father at the factory.
The battle moves away from the docks and the famous land mark of Osaka Castle is destroyed. Finally Godzilla gets the advantage and delivers a fatal bite to Angilas neck. In victory Godzilla unleashes his radioactive breath and huge areas of Osaka are set to flames.
The next day Tsukioka and Kobayashi visit the burned out shell of the tuna factory owned by Hidemis father. Theyve heard that the navy has lost track of Godzilla and offer to take their planes up and search for him
Tsukioka spots the creature heading for Shinko Island, Kobayashi takes off to help his. They spot Godilla ashore on the island. The air force develop a plan to bomb a section of the island stopping Godzilla from leaving again. This they believe will give them time to formulate a better way of dealing with the creature long term
As the two tuna planes continue to circle the island Kobayashi realizes the creature is heading back to the water. Flying his plane as low as possible he tries to distract it until the air force arrives. Eventually they do position for the attack but their bombs are not powerful enough.
Frustrated Kobayashi begins buzzing Godzilla again. Unfortunately he gets to close, the monster unleashes his ray damaging the plane. Kobayashi tries to fly out of trouble but crashes high up one of the mountains causing an avalanche.
The remaining air force planes realize that bombing the mountains will added to the avalanche caused by Kobayashis crash. Out of ammunition they planes need to return to base to reload before Godzilla can break free of the avalanche. The plan is to bring an entire mountain down on the creature and bury it
A detachment of infantry lands and attempts to set up a barrier of explosives before the creature escapes. They are only partially successful but create enough of a barrier to slow Godzilla till the air force arrives.
Finally three wings of fighter planes arrive and press home the attack. Despite taking heavy losses they manage to accomplish their mission and Godzilla is buried presumed dead