When the Japan Coast Guard investigates an abandoned yacht in Tokyo Bay, its 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 believes it was caused by a living creature, which is confirmed as news reports reveal its tail emerging from the ocean. Shortly thereafter, the creature moves inland, crawling through the Kamata district of Tokyo, leaving a path of death and destruction during a disorganized and chaotic evacuation. The creature quickly evolves into a bipedal form but overheats and returns to the sea.

The government officials focus on military strategy and civilian safety; Yaguchi is put in charge of a task force researching the creature. With high radiation readings from the creature's path, the task force realizes that it is energized by nuclear fission. The U.S. sends a special envoy, Kayoco Anne Patterson, who reveals that Goro Maki, a disgraced, anti-nuclear zoology professor, studied mutations caused by radioactive contamination, predicting the appearance of the creature. Maki was disbelieved by both American and Japanese scientific circles. The U.S. then prevented him from making his conclusions public. The abandoned yacht in Tokyo Bay belonged to Maki, who left his research notes, jumbled into a code, on the boat before disappearing.

The creature—named "Godzilla," after Maki's research—reappears in its fourth form, twice its original size, making landfall near Kamakura. The Japan Self-Defense Forces mobilize but prove ineffective as Godzilla breaks through their defenses into Tokyo. The U.S. intervenes with a massively destructive airstrike plan, prompting the evacuation of civilians and government personnel. Godzilla is wounded with MOP "bunker-buster" bombs but responds with destructive atomic rays fired from its mouth and dorsal plates, destroying a helicopter carrying the prime minister, along with top government officials and incinerating 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, theorizing that it could use a coagulating agent to freeze Godzilla. Analyzing tissue samples, it's discovered 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 in a few days; evacuations are ordered in multiple prefectures in preparation. Unwilling to see nuclear weapons detonated in Japan again, Patterson uses her political connections to buy time for Yaguchi's team, in which the interim government has little faith.

Yaguchi's team manages to decipher Goro Maki's encoded research using origami. The team adjusts its plan and procures the means to conduct its deep-freeze plan with international support. Hours before the planned nuclear attack, Japan enacts the deep-freeze plan. Godzilla is provoked into expending its atomic breath and energy against Predator and Reaper drones. The team then detonates nearby buildings and sends unmanned trains loaded with explosives toward Godzilla's feet, subduing it, and enabling tankers full of coagulant to inject it into Godzilla's mouth. Many are killed, but Godzilla is frozen solid.

In the aftermath, the fallout from Godzilla's attack is discovered to have a very short half-life, and Tokyo can soon be rebuilt. The international community agrees to cancel the nuclear attack on condition 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.