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A Japanese freighter sails along, just doing its thing while the sailors hang out on the deck. Suddenly, a flash of light erupts from the sea and sinks the vessel.
On dry, not-exploding land, Hideto Ogata is called in to help in the rescue operation. He has to cancel his date with his girlfriend, Emiko Yamane, but she's totally cool with it.
Another ship, the Bingo-maru, goes to investigate the destruction of the Eiko-maru. It also goes missing. A fishing vessel picks up three survivors from the Bingo-maru. Before they can get to safety, the fishing vessel also goes boom. It's just not a good day to be on a boat.
On Odo Island, villagers wait by the shore for the fisherman to return. One of the fishermen, Masaji Yamada, manages to sail in on a raft. He speaks incoherently of something large and terrifying in the ocean.
A reporter named Hagiwara arrives on the island to follow the story. While interviewing the villagers, some tell him about a mystical creature named Godzilla. That night, a typhoon beats down the island. It destroys several houses and kills several people and animals, including Masaji and his mother.
So far, not great.
A Diet committee is formed to investigate the problem. (There's always a committee.) They send zoologist Professor Kyohei Yamane and physicist Professor Tanabe to scientifically sleuth Odo Island. Tanabe finds several areas contaminated with radioactive fallout, while Yamane discovers a trilobite and footprints the size of homes. Godzilla appears on the far side of the island, and Yamane snaps a picture of it, the first bit of physical evidence for the creature's existence.
Yamane presents his findings to the committee. He believes the monster is a creature from the Jurassic period that was disturbed by U.S. H-bomb testing in the Pacific. Because…science? As debate ensues over how to deal with the information, ships continue to disappear at sea.
Hagiwara is tasked with interviewing a mysterious Dr. Serizawa, who's rumored to be doing research that could defeat Godzilla. The reporter asks Emiko if she will introduce them, since she's his fiancé. Emiko agrees, thinking it's a good time to tell Serizawa she loves Ogata and to break off their engagement.
Serizawa tells Hagiwara that his research has no bearing on the Godzilla problem. After Hagiwara leaves, Serizawa confides in Emiko what his research is about. Whatever he shows her in that totally-not-to-code lab terrifies her, and she leaves without breaking off the engagement.
That night, Godzilla attacks Shinagawa, destroying a passenger train and a bridge before returning to the ocean. With the military and its weapons having no effect on the creature, the Japanese Self-Defense Force decides to step up its game. They build a giant electrical fence around Tokyo Bay to keep Godzilla from reaching the populated areas.
One night, Ogata decides he will ask Yamane for permission to marry Emiko. Yamane returns home but is dismayed at the nation's desire to kill, rather than study, Godzilla. When Ogata suggests that killing the monster might be a good thing—because wanton death and destruction isn't his bag—the professor gets angry and tells him to leave. Ogata decides marriage talk isn't on the night's agenda.
Godzilla resurfaces. The monster's perturbed slightly by the electric fence but makes quick work of it with some atomic breath. Godzilla then rampages across Tokyo, razing the city until it's nothing but fiery rubble. Tanks and fighter jets try to fight it off but have no effect. Police and firefighters try to rescue the people but can do very little. Eventually, Godzilla returns to the sea.
Emiko volunteers at a field hospital with Professor Tanabe and tends to the wounded. When she is visited by Ogata, she decides to reveal that Serizawa has accidently uncovered a new form of energy and invented a machine for using it called the Oxygen Destroyer. With it, he can destroy the oxygen in an aquatic environment and kill all life there, but he'll continue to research it until he can find a proper, non-weaponized use for the technology.
Ogata goes to Serizawa and requests that he let him use the Oxygen Destroyer on you-know-who. Serizawa jukes him and runs to destroy his research. The two fight for a bit before deciding to talk it out. Serizawa believes the Oxygen Destroyer will only be used as a weapon if politicians discover it, while Ogata sees it as the only solution to the current disaster.
A news program comes on the TV, showing the destruction of Japan at Godzilla's hands, er, feet. Serizawa agrees to help Ogata, but he burns all of his notes and research. He'll use the Oxygen Destroyer this one time only.
A ship finds Godzilla's resting place in the ocean. Ogata and Serizawa suit up and dive into the ocean with the Oxygen Destroyer. On the ocean floor, they find Godzilla. Serizawa turns on the Oxygen Destroyer and gives Ogata the signal to retreat. However, Serizawa stays behind, severing his own line so they can't pull him up. Upon wishing Emiko and Ogata happiness, Serizawa dies so that his knowledge can't be used to create another Oxygen Destroyer.
Godzilla rises to the surface to escape the device's power, but it's too late. He gives one final roar before dying and sinking to the bottom. His bones rest on the ocean floor.
On the ship, everyone cheers Godzilla's defeat. Emiko and Ogata grieve for Serizawa. Worried over nuclear testing, Yamane wonders if another Godzilla will rise in the future.
Cue the sequels.