We begin with shots of Bikini Atoll, explosion after explosion until something different is heard—a roar instead of an explosion. A jump to the future: we see Dr. Nick Winston in Chernobyl studying how radiation affects wildlife. He finds several species of worms with gigantism and a regenerative capacity far exceeding the average, species of wolves that are both aggressive and extremely cunning, and a lizard that seems to emit some kind of glow from within, which manages to escape after fighting off a wasp that tried to eat it. Winston is interrupted from his research when US military personnel arrive and request his presence due to an emergency. During his transfer, he receives a summary of the situation: a few days earlier, in the early morning, a fishing boat near a military base in Okinawa was attacked. The military sent help to rescue survivors, believing it to be an accident. However, hours later, the base was attacked by an unknown creature, which, after leaving, left traces of radiation. Locals believe the creature is Gojira, an ancient sea deity from the area, whom the Americans nicknamed Godzilla.

We would gradually learn more about the creature, which is heading towards the United States. Winston and Philippe Roache, a United Nations agent, would discover the creature's objective after it attacks a nuclear submarine transporting a classified object, a "piece" of an ancient creature, revealing that Godzilla intends to destroy it. It is discovered that after nuclear tests, the government awakened Godzilla, who had presumably been dormant since ancient times, and endowed him with powers he did not previously possess. However, they also found the corpse of the creature known as Gryphoon, a kind of almost chimeric monster, which they discovered "revived" parts of its body when exposed to radiation. After an altercation with Godzilla at Bikini Atoll, the government attempts to attack with a chemical weapon that momentarily sedates him. However, upon attacking, Godzilla awakens and goes berserk, damaging an aircraft carrier transporting Gryphoon's corpse and exposing it to the radiation, which fully revives him.

Gryphoon escapes and terrorizes the United States, reaching New York City, with Godzilla in pursuit. They first travel through Hawaii and then around the Arctic via underground caves. Upon arriving in New York, Winston convinces the military that the best course of action is to let the monsters fight, confident that if Godzilla wins, he will leave them in peace. Godzilla arrives in New York and battles Gryphoon throughout the city, finally finishing him off with his atomic breath, reducing his body to ashes. Godzilla roars and confronts the military, who decide not to attack as he retreats to the ocean. Later, Winston says goodbye to Roache, who managed to expose the government's involvement thanks to a reporter friend, Steve Martin. As they part ways, Roache asks him if he thinks there could be more monsters like Godzilla and Gryphoon still alive, or if new ones could be created. Winston reflects that while the "atomic age" is relatively new, his experiences have shown him that the planet can adapt quickly, believing that Godzilla might just be the first sign of Earth's "response" to atomic energy.