In 1984, 3 months after an eruption at Daikoku Island, the Yahata Maru, a Japanese fishing boat, is lost in a storm at sea. When reporter Goro Maki (played by Ken Tanaka) comes upon the ship while sailing, he decides to investigate it. While the ship initially seems deserted, Maki soon makes a gruesome discovery: nearly all of the ship's crew are dead, as if they had been drained of fluids. After finding one survivor, Maki is attacked by a giant sea louse, which is soon killed by the survivor, Hiroshi Okumura (played by Shin Takuma). Maki speaks with Okumura, who tells him about a mountain that came to life the night before, when the sea lice attacked. After a search and rescue helicopter finds them, Okumura is taken to a hospital, where he is met by Professor Makoto Hayashida (played by Yosuke Natsuki). Hayashida has heard Okumura's story, and he shows him pictures, taken in 1954, of Godzilla.
Having heard Okumura's story, studying the remains of the sea louse, and seeing Okumura's reaction to the photographs, Hayashida comes to the conclusion that another Godzilla has appeared. With the realization that news of Godzilla's supposed return could cause mass panic, the Japanese government orders a temporary news blackout concerning the story of the Yahata Maru and her crew. Okumura's survival is to be kept secret from everyone except government officials as well, meaning that Maki's story won't be printed. When Maki hears about this, he is told by his editor to go see Professor Hayashida. While interviewing Hayashida, Maki meets a girl who he saw in a photograph that he pocketed off of Okumura. Hayashida reveals her to be Okumura's sister, Naoko (played by Yasuko Sawaguchi). Despite being told not to let Naoko learn of her brother's survival, Maki does so anyway. After Naoko reunites with her brother, she is shocked to learn that Maki simply used her to get pictures for his story.
Meanwhile, in Pacific Ocean, a Russian nuclear submarine is attacked and destroyed by Godzilla. Because neither Russia nor the US are aware of Godzilla's existence, the Soviets start pointing fingers at the United States, and the United States begin preparing for an attack from the Soviets, with both countries eager to wipe each other out. Realizing the very real possibility that World War III may erupt, the Japanese Prime Minister lifts the news blackout, and Godzilla's existence, including his attack on the Russian submarine, is revealed to the world. While this stops the Americans and the Russians from trying to blow each other up, the Japanese government must now contend with two nuclear superpowers who want to use their nuclear arsenal on Godzilla, which would involved using nuclear weapons near or in Japan. The JSDF begins patrolling the waters around Japan, searching for Godzilla. Soon, after Godzilla's existence is revealed, and Maki's story is printed, Godzilla finally makes landfall on the coast of Japan, attacking a nuclear power plant, feeding off of the reactor. Maki, Hayashida, and Okumura are present to witness the attack and take photographs; however, Godzilla soon leaves rather abruptly while feeding, leaving everyone bewildered by his sudden exit.
The news media are now in a frenzy reporting on Godzilla after his attack, and the United States and Russia are even more eager to destroy the monster. Looking over the photographs that they took during Godzilla's attack, Okumura notices that Godzilla was following a flock of birds. Believing Godzilla to be a dinosaur of some kind, and knowing that dinosaurs and birds are closely related, Hayashida hypothesizes that Godzilla may possess some kind of homing instinct, which was triggered by a frequency produced by the cries of the birds. He proposes a solution to the Japanese government that they create a device to produce this frequency so that they can lure Godzilla anywhere that they want. Mt. Mihara on Oshima Island is chosen as Godzilla's tomb. Okumura is sent to the site alongside Professor Minami (played by Hiroshi Koizumi) and preparations are made for a controlled eruption.
Soon, representatives from the United States and Russia arrive for a conference in Japan, wherein the Prime Minister (played by Keiju Kobayashi) forces the representatives to understand his country's position by asking them if they would be willing to use nuclear weapons on Godzilla if he were to attack their own soil. He tells this to his Foreign Affairs Minister (played by Mizuho Suzuki) after the meeting is over. Meanwhile, the Russian freighter Balashevo has docked in Tokyo Bay, and it is carrying a launch device for a nuclear missile satellite in space. Meanwhile, a JSDF patrol helicopter soon spots Godzilla making a B-Line for Tokyo. The JSDF begin preparing for Godzilla's arrival, setting up tanks, mortars, rockets, missiles, and even jets.
Later that night, Godzilla finally appears, with a formation of jets being the first line of defense. The jets prove useless as Godzilla destroys several of them and then dives under the water before resurfacing closer to the main defense line. Godzilla proves himself to be impervious to all of the military's weaponry. The JSDF soon prepare to launch the Super-X, a VTOL that was designed in secret to protect the capital, to attack Godzilla using cadmium. Unfortunately, the cadmium shells are still being loaded when Godzilla attacks. Speaking of Godzilla, the titular saurian quickly makes short work of the JSDF defense line with his atomic ray, killing hundreds of troops and destroying dozens of vehicles before he leaves the water. During his attack, the waves produced by Godzilla cause the Balashevo to crash against the docks, killing much of its crew and accidentally causing the launch timer to activate. Maki soon visits Hayashida's lab to get him and Naoko to evacuate, but they are still working on the tape to lure Godzilla, with Hayashida believing it to be the only solution to effectively stop Godzilla, although he doesn't actually believe that Godzilla will die either way.
Godzilla soon makes his way into Yurakucho, where the military tries to stop him to no avail, and Godzilla continues leaving a path of death and destruction in his wake. Meanwhile, back at the Balashevo, the ship's captain tries desperately to stop the missile from launching, but he is killed by a explosion onboard, and the missile soon launches. The Japanese government quickly gets word of this, just as Godzilla walks over their bunker. The Americans launch their own missile to shoot down the Soviet missile. The monster soon makes his way into Shinjuku, and is met with maser fire, which does nothing to stop him as he continues to destroy the city, and the Super-X is finally launched. Godzilla soon appears near Hayashida's laboratory, where Hayashida tests the device on Godzilla. The device works, but when a maser cannon disrupts the tranquility, Godzilla resumes his destructive path, damaging the Bio-Physics Institute, forcing the three people inside to improvise an escape until the Super-X finally arrives. The Super-X manages to inject Godzilla with three cadmium shells, sending the beast crashing into a building, where he enters a coma-like state.
Despite Godzilla's current state, Hayashida believes that the monster isn't dead yet, and a large crowd of people has gathered near the monster's "corpse." A helicopter carrying Okumura soon arrives in Tokyo, and Hayashida and Okumura take the finished tape to Oshima Island, leaving Maki and Naoko behind, allowing the two of them to reconcile. Soon, the Soviet missile is intercepted thousands of feet in the air over Tokyo by an American missile, with the atmospheric explosion creating an EMP, causing the Super-X to settle down near Godzilla while repairs are made. After communications and electrical systems are restored, a storm appears overhead, sending lightning strikes that hit Godzilla, reviving him. People are soon running for their lives as Godzilla proves himself to be nearly immortal, and he soon resumes his battle with the Super-X. The Super-X has run out of cadmium, so its crew must resort to lasers and other weaponry in its battle against Godzilla, turning much of Tokyo into a raging inferno as Godzilla seeks revenge for the Super-X's earlier transgression. The Super-X resists several atomic rays from Godzilla, but it cannot prevail forever, and soon a fire breaks out in the cockpit, forcing the Super-X to set down. Godzilla then topples a building onto the Super-X, destroying the machine and killing its crew. Now, with Hayashida's frequency tape being humankind's only hope, Naoko and Maki desperately try to escape the destroyed city, but Godzilla has caused so much damage that they don't even know what street they're on anymore. As the two humans find themselves facing death by Godzilla's foot, the monster pauses his actions and suddenly turns around, departing Tokyo and heading for Oshima Island. Everyone who's still alive breathes a collective sigh of relief, for Hayashida's plan has worked.
Godzilla soon leaves the ruined city and swims toward Oshima Island, drawn by the frequency. He soon nears the top of Mt. Mihara, where dozens of explosives have been placed, both near the top and deep inside the bowels of the volcano. As soon as Godzilla is in position, Okumura detonates the explosives, causing an eruption. Godzilla lets out one last roar, one which contains not defiance, but perhaps sadness. Either way, Godzilla soon falls into the pit of Mt. Mihara, allowing himself to be swallowed by the volcano as mankind somberly revels in its narrow victory, one which may only be temporary.