An iguana nest is exposed to the fallout of a military nuclear test in French Polynesia. In the South Pacific Ocean, a Japanese fishing vessel is suddenly attacked by a giant creature, with only one fisherman surviving. Dr. Niko “Nick” Tatopoulos, an NRC scientist, is in the Chernobyl exclusion zone researching the effects of radiation on wildlife, but is interrupted by an official from the U.S. State Department. In Tahiti, a mysterious Frenchman questions the traumatized survivor over what he witnessed, who repeatedly replies “Gojira.” Nick is sent to Panama and Jamaica to study a trail of wreckage leading to the recovered Japanese fishing ship with massive claw marks on it. Nick identifies skin samples he discovered in the shipwreck as belonging to an unknown species. He dismisses the military’s theory that the creature is a living dinosaur, instead deducing it is a mutant created by nuclear testing.
The creature travels to New York City, leaving a path of destruction in its wake. The city is evacuated before the U.S. military, on Nick’s advice, lure the creature into revealing itself with a large pile of fish. Their attempt to kill it fails, however, and only causes further damage before it escapes. Nick collects a blood sample, and by performing a pregnancy test, discovers the creature reproduces asexually and so is collecting food for its offspring. Nick also meets up with his ex-girlfriend, Audrey Timmonds, a young aspiring news reporter. While she visits him, she uncovers a classified tape in his provisional military tent concerning the monster’s origins and turns it over to the media. She hopes to have her report put on TV as to launch her career, but her boss, Charles Caiman, uses the tape in his report, declaring it his own discovery, and dubs the creature “Godzilla.”
As a result, Nick gets removed from the operation and he disowns Audrey, before getting kidnapped by the mysterious Frenchman Philippe Roaché. Revealing himself as an agent of the French secret service, Philippe explains that he and his colleagues have been closely watching the events to cover up their country’s role in the nuclear testing that created Godzilla. Suspecting a nest somewhere in the city, they cooperate with Nick to trace and destroy it. Meanwhile, Godzilla resurfaces and dives into the Hudson River to evade a second attempt by the military to kill it, where it is attacked by Navy submarines. After colliding with torpedoes, Godzilla sinks, believed to be dead by the authorities.
Nick and Philippe’s team, followed by Audrey and her cameraman Victor “Animal” Palotti, find the nest inside Madison Square Garden, with over 200 eggs. The eggs begin to hatch and the strike team are attacked by the offspring. Nick, Animal, Audrey and Philippe take refuge in the Garden’s broadcast booth and successfully send out a live news-report to alert the military. A prompt response involving an airstrike is initiated as the four escape moments before the Air Force bomb the arena.
Audrey and Nick reconcile, before the adult Godzilla, having survived, emerges from the Garden’s ruins. Enraged by the deaths of its brood, it takes its rage out on the four, chasing them across Manhattan. After a taxi chase, they manage to trap Godzilla within the cables of the Brooklyn Bridge, allowing the returning Air Force to shoot it. Godzilla dies from its wounds, and the remaining citizens and authorities celebrate. Audrey tells Caiman that she quits working for him after what he did, before leaving with Nick. Philippe, taking a tape Animal was recording and promising to return it after removing certain contents, thanks Nick for his help and parts ways. In the ruins of Madison Square Garden, a single surviving egg hatches and the hatchling roars.