When the Japan Coast Guard investigates an abandoned yacht in Tokyo Bay, their boat is destroyed and the Tokyo Bay Aqua-Line is flooded. After seeing a viral video of the incident, Deputy Chief Cabinet Secretary Rando Yaguchi theorizes that it was caused by a living creature. His theory is confirmed when news reports show a massive tail emerging from the ocean. Shortly thereafter, the creature moves inland and crawls through the Kamata district of Tokyo in the midst of inadequate evacuation. The creature leaves a path of destruction and numerous casualties, and evolves into a bipedal red-skinned form before it begins to overheat and returns to the sea. The government officials focus on military strategy and civilian safety, while Yaguchi is put in charge of a task force to research the creature. Due to high radiation readings, the group theorizes that it is energized by nuclear fission. The U.S. sends a special envoy, Kayoco Anne Patterson, who reveals that a disgraced, vehemently anti-nuclear zoology professor, Goro Maki, had been studying mutations caused by radioactive contamination and theorized the appearance of the creature, but he is disbelieved by both American and Japanese scientific circles. The U.S. then prevented him from making his conclusions public. The abandoned yacht discovered in Tokyo Bay was Maki’s, and he left his research notes, jumbled into a code, in the boat before disappearing.

The creature, named Godzilla after Maki’s research, reappears, now twice its original size, and makes landfall near Kamakura en route for Tokyo. The Japan Self-Defense Forces mobilize, but their attacks have no effect and they are forced to withdraw when Godzilla breaks through their defenses into the city. The U.S. intervenes with a massively-destructive air strike plan, prompting the evacuation of civilians and government personnel. U.S. B-2 bombers wound Godzilla with MOP “bunker-buster” bombs. Godzilla recovers quickly and responds with highly destructive atomic rays fired from its mouth and dorsal plates, which hit and destroy the helicopter carrying the top government officials, and all of the B-2s, as well as incinerating and irradiating large swaths of Tokyo. Depleting its energy, Godzilla enters a dormant state and becomes immobile. Yaguchi’s team discovers that Godzilla’s plates and blood work as a cooling system and theorize that they could use a coagulating agent to freeze it. After analyzing tissue samples, they find that Godzilla is an ever-evolving creature, able to reproduce asexually. The United Nations, aware of this, informs Japan that thermonuclear weapons will be used against Godzilla should the Japanese fail to subdue it on their own in a few days. Evacuations are ordered in multiple prefectures in preparation for the nuclear attack. Unwilling to see nuclear weapons detonated in Japan again, Patterson uses her political connections to buy time for Yaguchi’s team, who the interim government has little faith in.

Yaguchi’s team has a breakthrough when they decipher Goro Maki’s encoded research. They adjust their plan and procure the means to conduct their deep freeze plan with international support. Mere hours before the planned nuclear attack, Japan enacts the deep freeze plan. Godzilla is provoked into expending its atomic breath and energy against American drones. The team then detonates explosives in nearby buildings and in trains sent towards Godzilla’s feet, knocking the monster down and giving tankers full of coagulant an opportunity to inject it into Godzilla’s mouth. Though many are killed in the process, Godzilla is frozen solid. In the aftermath, it is discovered that the Godzilla fallout has a very short half-life and that Tokyo can soon be reconstructed. The international community agrees to cancel the nuclear attack but has the new Japanese government agree that, in the event of Godzilla’s reawakening, an immediate thermonuclear strike will be executed. On Godzilla’s tail, humanoid creatures appear frozen in the process of emerging.