In 1954, a series of mysterious ship sinkings in the Pacific draws a small group of people to Odo Island. Among them are Shinkichi Morita, whose brother was lost at sea, Emiko Yamane, and her father, Professor Kyōhei Yamane, a renowned paleontologist. The island's elderly residents speak of a legendary sea dragon called Godzilla, a myth that turns horrifyingly real when the creature emerges from the depths. Revealed to be a prehistoric reptile, an intermediate form between marine and terrestrial reptiles, Godzilla has been mutated and awakened by American hydrogen bomb tests in the Pacific. The creature is nearly indestructible, possessing incredible resilience, a radioactive atomic breath described as a beam of white-hot fire, and an apparent immortality born of surviving for over two million years at the bottom of the ocean.

The narrative follows three central characters as they react to this catastrophe. Shinkichi, a young man from the post-war generation, is driven by a desire for revenge against the beast that destroyed his family. Professor Yamane, in contrast, becomes fascinated by Godzilla. He argues that the creature should be studied, not destroyed, believing that unlocking the secrets of its cellular regeneration could be a scientific miracle that would allow Japan to atone for its war crimes by sharing this discovery with the world. Emiko is caught between these two perspectives and is also bound by a secret engagement to a brooding and disfigured chemist, Doctor Daisuke Serizawa. As Godzilla makes landfall in Tokyo, wreaking unimaginable destruction on the metropolitan center, the government scrambles for a solution. Desperate, Emiko reveals Serizawa's secret to Shinkichi: the Oxygen Destroyer, a terrible new weapon that breaks down oxygen molecules, destroying all life in a given area and reducing even Godzilla's tough hide to a skeleton. Serizawa, tormented by the potential for his invention to be used as a new superweapon, agrees to use it one final time. He activates the device, killing Godzilla in Tokyo Bay. Serizawa then cuts his own lifeline, committing suicide to ensure the secret of the Oxygen Destroyer dies with him.

One year later, the world faces a second crisis in Godzilla Raids Again. Fishery pilots Kōji Kobayashi and Shōichi Tsukioka are flying over the ocean when they witness a terrifying battle between two colossal monsters: a second Godzilla and a spiky, four-legged creature identified by Professor Yamane as Anguirus, an ancient ankylosaur-like rival. The two kaiju clash in a furious brawl, destroying much of Osaka before Godzilla kills Anguirus. Professor Yamane delivers a grim warning: without the Oxygen Destroyer, there is nothing humanity can do to stop this second Godzilla. The story shifts focus to the pilots and Hidemi, the daughter of their company president, as they attempt to track the creature. The military attempts conventional attacks, but Godzilla proves impervious to their firepower. The narrative arc concludes with a desperate plan. Tsukioka and Kobayashi use their planes to lure Godzilla to a remote northern island. In a final gamble, they trigger massive explosions, causing an avalanche of ice and rock that buries Godzilla in a frozen tomb. The novel ends on an ambiguous, somber note, suggesting that while the immediate threat is gone, Godzilla may not be dead, merely sleeping beneath the ice, a persistent and terrifying force of nature.