In Tokyo Bay, the Japanese Coast Guard investigates an abandoned yacht, only to have its boat destroyed by something massive beneath the surface. Shortly after, the Tokyo Bay Aqua-Line is flooded and collapses. Deputy Chief Cabinet Secretary Rando Yaguchi, after viewing a viral video of the incident, becomes convinced the destruction was caused by a living creature, a theory initially dismissed by his superiors until a massive tail emerges from the ocean.

The creature soon makes landfall, moving through the city in a crawling form and leaving a path of devastation and civilian casualties before evolving onto two legs and retreating to the sea. As top government officials focus on military strategy and civilian safety, Yaguchi is put in charge of a task force to research the creature. High radiation readings lead the team to theorize the being is energized by nuclear fission. The United States sends a special envoy, Kayoko Anne Patterson, who reveals that a disgraced zoology professor named Goro Maki had been studying mutations caused by radioactive contamination and had theorized the creature's appearance, but the U.S. covered up his research. The abandoned yacht in Tokyo Bay belonged to Maki, who left his investigation notes there before disappearing.

The creature, now named Godzilla after Maki's research, reappears at twice its original size and makes landfall near Kamakura, heading for Tokyo. The Japan Self-Defense Forces mobilize, but their conventional attacks have no effect and they suffer major casualties. The U.S. intervenes, with bombers attacking Godzilla, but the creature is barely injured and responds with highly destructive atomic rays fired from its mouth and dorsal fins. The battle destroys a large part of Tokyo and also downs the helicopter carrying most of Japan's top government officials. After depleting its energy, Godzilla enters a dormant, immobile state.

Yaguchi's team discovers that Godzilla's fins and blood function as a cooling system, leading them to theorize that a coagulating agent could trigger a reaction to freeze the creature. Analyzing tissue samples, they also find that Godzilla can survive as long as air and water are available and is capable of reproducing asexually. Aware of this threat, the United Nations, led by the U.S., informs Japan that the use of thermonuclear weapons against Godzilla is inevitable. Unwilling to see nuclear weapons detonated in Japan again, and risking her career, Patterson uses her political connections to buy Yaguchi's team as much time as possible to complete their plan.

Against intense international pressure and a lack of faith from the interim government, the team manages to procure enough coagulant and enacts their risky plan. They provoke Godzilla into using its atomic breath until it weakens, then detonate explosives in nearby buildings to knock the creature off balance, bringing its head down to near-ground level so the coagulant can be injected directly into its mouth. Though many are killed in the process, the plan succeeds and Godzilla is frozen solid. In the aftermath, the international community calls off the nuclear strike, but forces the new Japanese government to agree that a thermonuclear bomb will be launched immediately if Godzilla ever reawakens. A final, haunting shot of Godzilla's tail reveals humanoid skeletal figures frozen in the middle of emerging from the flesh.