In 2016, the investigation by the Japan Coast Guard begins when an abandoned yacht is found in Tokyo Bay, marked by the destruction of its boat and a chilling scene where blood floods the Aqua-Line. After Deputy Chief Cabinet Secretary Rando Yaguchi views a disturbing viral video of the event, he suspects that a living creature is responsible for the chaos, a theory soon validated as news reports surface, showcasing the creature’s tail emerging ominously from the ocean. As panic ensues, the creature begins its deadly advance inland, crawling through the bustling districts of Kamata and Shinagawa, devastating everything in its path during a tumultuous evacuation.
As the creature undergoes rapid evolution, transforming into a bipedal form, it becomes overheated and retreats back into the sea. In response to the mounting crisis, government officials prioritize military strategy and civilian safety, appointing Yaguchi to lead a special task force dedicated to investigating this terrifying new entity. The task force soon discovers alarming radiation levels along the creature's path, signaling its energy source as nuclear fission. An unexpected collaboration arises when the U.S. sends envoy Kayoco Anne Patterson, who reveals crucial information about Goro Maki, a once-disgraced anti-nuclear zoology professor. Maki’s groundbreaking research on mutations stemming from radioactive exposure had predicted this creature's emergence, but was disregarded by both American and Japanese scientific communities. Furthermore, it is uncovered that Maki had left behind his research notes, cryptically encoded, on his abandoned yacht before vanishing.
Re-emerging in its formidable fourth form, Godzilla—named after Maki's studies—lands near Kamakura, prompting a swift mobilization of the Japan Self-Defense Forces. Unfortunately, despite their efforts, they find themselves outmatched as Godzilla breaks through their defenses and storms into Tokyo. In an attempt to quell the rampage, the U.S. devises a destructive airstrike plan, forcing the evacuation of civilians alongside governmental officials. Armed with fortifying MOP "bunker-buster" bombs, Godzilla is temporarily incapacitated but retaliates fiercely, unleashing its atomic breath, resulting in catastrophic destruction—including the demise of a helicopter carrying the prime minister and other key leaders—consuming vast portions of Tokyo. Ultimately, weakened and drained, Godzilla retreats into a state of hibernation.
Yaguchi's diligent team uncovers that the creature's plates and blood serve as a natural cooling system and postulates that a coagulant could be deployed to freeze Godzilla. While examining samples of its tissue, they learn that Godzilla possesses the ability to evolve continuously and even reproduce asexually. Alarmed by this development, the United Nations cautions Japan that thermonuclear weapons will be employed against Godzilla if it’s not subdued promptly; hence, mass evacuations are ordered across several prefectures. Amidst the rising tensions, Patterson appeals to her political contacts to buy time for Yaguchi’s team, which has seen dwindling support from their interim government.
Utilizing origami, Yaguchi's team finally decodes Maki's research, which helps refine their strategy to implement an international deep-freeze initiative. Just hours prior to the anticipated nuclear strike, Japan enacts its plan. Godzilla is incited into using its atomic breath against the attacking Predator and Reaper drones. Yaguchi's team orchestrates urban explosions and reroutes unmanned trains laden with explosives towards Godzilla’s feet, managing to subdue it briefly, facilitating the injection of coagulant through its mouth. Many lives are lost during this risky operation, yet ultimately, Godzilla is rendered solidly frozen.
The aftermath reveals that Godzilla’s isotopic composition possesses a half-life of 20 days, suggesting a pathway for Tokyo’s eventual restoration. The international community agrees to retract the nuclear attack with the condition that should Godzilla ever awaken again, an immediate thermonuclear response will follow. In a haunting twist, frozen humanoid figures are discovered emerging from Godzilla’s tail, hinting at more challenges to come.
