United Nations reporter Eric Carter reports about earthquakes in Chile and the efforts to provide relief to the victims. In an unrelated story, the Bering Sea is experiencing an unusually warm temperature, causing icebergs to break up and drift southward. UN submarine Sea Hawk has been sent to investigate the phenomenon with some of the world's top scientists onboard. In a third story, Dr. Akiro Makino has discovered a new berry on a small, remote island in the South Pacific, which produces a mild narcotic effect. The natives of the island, however, refuse to part with many of the berries because they use them to placate their mysterious god, some sort of giant creature. Makino's employer, Pacific Pharmaceuticals, says there is such a god and that the reason he is a giant is because he eats the berries.
Dr. Makino meets with his boss, Mr. Tako, discussing the berries and the natives' god. He shows Mr. Tako the island, called Faro, on a chart. Mr. Tako's aides, Sakurai and Kinsaburo, doubt that there is a monster god, joking that they must really need publicity. Flipping a coin, Mr. Tako orders the men to go to Faro and find the monster. He wants a monster to boost the company's failing TV program. Whether the monster exists or not, he tells them to find it.
That night at Sakurai's apartment, his sister Fumiko and her boyfriend Fujita eat dinner with Sakurai. Fujita shows Sakurai his new invention, an incredibly strong wire thread, displaying its strength by climbing over the apartment balcony, supported only by the thread. He convinces Sakurai to take some of the thread with him on his expedition.
In the Arctic Ocean, the submarine Sea Hawk enters the area of the unusual temperatures. The captain sights a strange iceberg emitting a glowing light. Scientists onboard state that it resembles the Khelenkoff light generated in nuclear reactors. The iceberg is also affecting their Geiger counter. The sub draws closer, hitting the iceberg and causing its surface to crumble away. The sub begins to take on water and distress calls are sent. As water enters the bridge, a terrible roar is heard and flames engulf the doomed submarine.
A US Navy rescue helicopter is sent to find Sea Hawk. They find the sub's beacon dye around the iceberg and descend for a closer look. Both pilots are horrified when the face of the iceberg breaks away and Godzilla emerges.
The news of Godzilla's survival stuns the world. As Eric Carter reports, Godzilla is heading straight toward Japan. Dr. Shigezawa tries to calm reporters, assuring them that the army will stop Godzilla and that the atom bomb is being considered as a last resort.
Godzilla attacks a military base in the north of Japan, unharmed by the concentrated fire of tanks and missile batteries. The monster soon lays waste to the entire installation.
All of the press Godzilla is getting enrages Mr. Tako, who sends a wire to Sakurai and Kinsaburo, demanding that they quickly find him his own monster. At sea, the Pacific Pharmaceuticals ship sights Faro Island. As Kinsaburo, Sakurai and their translator Kono land on Faro, a party of native warriors surrounds them. Virtually taken prisoner, the men are taken back to the village and the warriors' chieftain.
Kono parlays with the chief, who angrily demands that the men leave Faro. A gift of cigarettes and a transistor radio changes the chief's mind and he allows the men to stay. He will not be responsible, however, if their monster god comes down from the mountains and eats them. Kinsaburo is all in favor of leaving after hearing this.
Suddenly lightning cracks overhead and the natives quickly begin to pray to their god. Sakurai laughs, concluding that their god is nothing but lightning. Soon, a horrible roar echoes down to the village, frightening even Sakurai. Kinsaburo drops to his knees to join the natives in placating their terrible god.
Back in Japan, Fumiko gets news that the plane Fujita was taking to Hokkaido has crashed. Hoping that he may be among the survivors, Fumiko decides to go to Hokkaido. At the same time, UN reporter Yataka Omura announces that Godzilla is heading toward Hokkaido and the area is being evacuated. In New York, Eric Carter interviews Dr. Johnson, a paleontologist, who tries to offer some theories on Godzilla's origins and his survival into the present day. In an unrelated story, the Pacific Pharmaceuticals team has claimed to have heard the cries of the monster god of Faro Island.
Sakurai and Kinsaburo lead a group of natives into the interior of Faro Island. They are just getting near the mountains when Kinsaburo begins complaining about his corns, claiming they always hurt when near monsters. Kinsaburo panics when he finds a large lizard. Sakurai shoots the creature, but as he does so, the horrible roars are again heard and a landslide threatens the men. Terrified, the group flees back to the village.
That night, the villagers continue to pray at their shrine. In their hut, Kinsaburo seems feverish, complaining about his corns. Kono sends a native boy to get some of the natives' red berry juice for Kinsaburo. The boy sneaks to the hut where the juice is stored. At the same time his mother searches for him. She catches the boy in the hut but before she can scold him, the structure is attacked. A giant octopus has slithered out of the sea and is intent on getting the juice inside the hut. The alarm goes out and the entire village attacks the octopus with torches and spears, Sakurai and Kinsaburo helping out with their rifles. The boy and his mother escape, but there seems to be no stopping the octopus.
Again the terrible cry echoes across Faro. A huge gorilla appears on the far side of the massive log wall that protects the village. King Kong makes short work of the wall, hurling the mass of timbers at the octopus. Kong advances, grappling with the mollusk. Hurling it away from him, Kong drives the creature away by throwing huge boulders at it.
King Kong turns away from the retreating octopus, smelling the natives' berry juice. He picks up the huge jars of juice they had left for him as an offering and begins to guzzle it down. As Sakurai predicts, the juice soon puts Kong to sleep. The monster falls to the ground and the natives dance and sing around their monster god, seranading him in his slumber. The sight of King Kong is too much and Kinsaburo again begs Sakurai to leave the island. Sakurai assures him that they will. But there is a catch, one which shocks Kinsaburo. They are leaving faro, but they are taking Kong with them.
The discovery of King Kong stuns the world. Dr. Johnson comments on the differences between Kong and Godzilla. He says that they may be instinctive rivals. Although Godzilla has disappeared, he is certain that when Godzilla does return, he will do so in Japan. Omura reports that the army has been fully mobilized to deal with Godzilla. As for Kong, Japanese authorities have no intention of allowing the monster to be brought to the mainland.
At sea, the Pacific Pharmaceuticals ship tows a huge log raft on which the slumbering King Kong has been tied. A helicopter arrives, lowering Mr. Tako to the ship's deck. With a cry of 'Banzai' Mr. Tako joins Sakurai and Kinsaburo. Mr. Tako beams as he sees Kong, moving to get a closer look. He rests his hand on the plunger which is wired to the explosives lining the raft. Sakurai and Kinsaburo warn Mr. Tako of what he has done and he carefully removes his hand, only to almost repeat the gesture. Just then, a Japanese coast patrol boat meets the ship. Mr. Tako is given orders to return Kong to Faro Island at once, as Kong is regarded as a menace to Japan. Thinking of all of the commitments he has made for Kong to appear on TV, Mr. Tako faints upon receiving this news.
Fujita appears outside Fumiko's apartment. He missed his flight. Fumiko's neighbor, Tamiye, tells Fujita that Fumiko has gone to Hokkaido to look for him. Unfortunately, Godzilla has also been reported near Hokkaido. Fujita races away to try and intercept Fumiko's train. The train rumbles across the countryside, unaware that Godzilla has returned to land and is already in the train's path. Worse, Godzilla is attracted by the train lights. The train screeches to a stop as the conductor becomes aware of the peril and the passengers flee into the countryside, scrambling aboard any vehicle they can find. Fumiko is unable to fight her way through the panicked mob and is left on foot.
Fujita ignores army roadblocks, driving his jeep toward the train in hopes of finding Fumiko. Godzilla makes short work of the train and lumbers on, following the tracks. Fumiko tries to escape across the wilderness. Fujita finds her and the pair hide as Godzilla's massive form passes.
Back on the Pacific Pharmaceuticals ship, King Kong awakens, trying to escape his restraints and threatening to sink the ship. The captain orders the raft cut away, but the ship is still no safer. Sakurai and Kinsaburo try to blow the raft up, despite Mr. Tako's attempts to stop them. In the struggle, it is Mr. Tako himself who presses down the plunger, but it fails to blow up the raft. Sakurai and Kinsaburo try to shoot the dynamite with rifles and succeed at last, blowing the raft to bits. When the smoke clears, however, Kong rises from the water, roaring and unharmed by the explosion.
King Kong is reported heading across Japan in a direction which puts him on an interception course with Godzilla. Dr. Johnson speculates that Kong can sense the other monster and is instinctively seeking out his rival. Mr. Tako, Sakurai and Kinsaburo drive to the Nasu Plain, where Kong and Godzilla will meet. They join the army in watching the monsters draw close. The monsters roar at each other, but Godzilla's display of fiery breath as he destroys a passing helicopter seems to intimidate Kong. The giant ape hurls boulders at Godzilla. Godzilla responds by singing Kong with his breath. Despite Mr. Tako's shouts of encouragement, Kong retreats before Godzilla's radioactive breath.
General Shinzo orders an enormous pit dug and lined with explosives and poison gas. Rivers and streams will be doused with gasoline and set afire to draw Godzilla into the trap. The pit is concealed and as night descends, the monster stalks toward the pit. The camouflage works, and Godzilla falls into the hole. Explosions shake the ground as the dynamite ignites, after which there is silence. Observers draw closer to the pit, only to retreat when Godzilla emerges. Neither dynamite nor poison gas has been enough to stop him.
A blockade of high-tension wires is hastily established around Tokyo, based on Godzilla's shying away from power lines during his attack on the train. Dr. Johnson states that while the tactic may stop Godzilla, King Kong draws strength from electricity and the blockade will not stop Kong. Godzilla reaches the line of towers, plowing into the electrified lines. Shocked by the surging electricity, Godzilla retreats from the blockade.
Just at that moment, news reaches General Shinzo that King Kong has entered Tokyo. Evacuation of the city begins as Kong rampages closer to the blockade line. The power lines do not stop the ape, who seems to feed on the electricity. Fujita and Fumiko attempt to evacuate but are separated at the train, which leaves Fujita on the station platform. Kong prowls deeper into Tokyo. Seeing the train, he grabs it, lifting it high into the air. Kong snatches Fumiko from the traincar, dropping the rest of the train. Kong carries the screaming woman to the Diet building, which he quickly climbs. The army surrounds Kong, blinding him with searchlights.
Before General Shinzo can order the attack, Sakurai arrives, pointing out that Kong has his sister. Shinzo verifies Sakurai's claim, but says that he can't hold his fire for long. Kong must not be allowed to escape. Sakurai and Kinsaburo hatch a plan to stop Kong. They will load the berry juice into the warheads of rockets and explode them over Kong. The resulting fumes will put him to sleep. Loudspeakers will play a recording of the Faro Islanders' chanting while Sakurai beats the rhythm on a set of drums.
The plan proceeds flawlessly and Kong topples to the ground. Fujita rescues Fumiko from the sleeping monster's hand. Fumiko is rushed to a hospital. Godzilla is reported near Mt. Fuji. The Prime Minister states that the atomic bomb is out of the question. Japan's only hope is to bring Kong and Godzilla together and hope that both will die in the resulting conflict. Fujita's wire will be used to bind Kong so that he can be lifted by giant balloons and flown to Mt. Fuji. The still slumbering Kong is towed by helicopters over Tokyo. Sakurai and Fujita follow the monster in another helicopter.
Soon, the airlift reaches Mt. Fuji. Godzilla is sighted below and the cables binding Kong are cut. The revived ape drops to the slope of Mt. Fuji, sliding down the slope and crashing into Godzilla. The two monsters proceed to fight, Godzilla's brute strength against Kong's cunning. The battle goes back and forth until Kong strikes his head against a large rock. Godzilla kicks more boulders onto the stunned ape, burying him. Godzilla then ignites the surrounding trees, hoping to roast the giant ape. Just then, an electrical storm passes overhead. Several lightning bolts snake downwards, striking Kong's body and reviving him. The restored monster attacks Godzilla once more, electricity flowing from his fingers to shock Godzilla each time he grabs the reptile. Filled with power, Kong is oblivious to Godzilla's fiery breath, ignoring Godzilla's powerful blasts.
The battle continues, the two monsters devastating an ancient castle that stands in their way. At last, the two titans grapple and fall over the side of a cliff. The monsters' undersea conflict causes an earthquake and a tidal wave to ravage the coast. Soon the sea grows calm again. King Kong resurfaces, swimming out to sea. There is no sign of Godzilla. As Eric Carter reports, strangely enough, Kong is wished luck on his long journey home.