Following a nuclear incident in French Polynesia, a lizard's nest is irradiated by the fallout of subsequent radiation. Decades later, a Japanese fishing vessel is suddenly attacked by an enormous sea creature in the South Pacific ocean; only one seaman survives. Traumatized, he is questioned by a mysterious Frenchman in a hospital regarding what he saw, to which he replies, "Gojira".
Manhattan, where much of the destruction unfolded.
Dr. Niko "Nick" Tatopoulos (Broderick), an NRC scientist, is in the Chernobyl exclusion zone in Ukraine researching the effects of radiation on wildlife, but is suddenly interrupted by the arrival of an official from the U.S. State Department.
He is sent to Tahiti and Jamaica, escorted by the military, to observe the wreckage of the recovered Japanese fishing trawler with massive claw marks on it. The Frenchman is also present, observing the scene, and introduces himself as Philippe Roaché (Reno), an insurance agent. Aboard a military aircraft, Dr. Tatopoulos 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 that it is a mutant created by nuclear testing.
The large reptilian creature dubbed as "Godzilla" by the media, travels to New York City leaving a path of destruction in its wake. The city is evacuated as the military attempts to kill it but fails in an initial attempt. Dr. Tatopoulos later collects a blood sample and learns that Godzilla reproduces asexually and is collecting food for its offspring. Aspiring journalist and ex-girlfriend of Dr. Tatopoulos, Audrey Timmonds (Pitillo), uncovers a classified tape in his provisional military tent which concerns the origins of the lizard. Her superior Charles Caiman (Shearer) however, declares the tape as his own media discovery.
The tape is broadcast on television embarrassing the military on the sensitive nature of the situation. Dr. Tatopoulos' team is kidnapped by Roaché, who reveals himself to be an agent of the DGSE, the French foreign intelligence agency. He and his colleagues have been keeping close watch on the events and are planning to cover up their role in the nuclear accident that spawned the creature. Suspecting a nest somewhere in the city, they cooperate with Dr. Tatopoulos to trace and destroy it.
Following a chase with Godzilla, the creature dives into the Hudson River where it is attacked by Navy submarines. After sustaining head-on collisions with torpedoes, the beast sinks after being rendered incapacitated. Believing it is finally dead, the authorities celebrate. Dr. Tatopoulos and Roaché's special operations team, covertly followed by Timmonds and her cameraman Victor "Animal" Palotti (Azaria), make their way through underground subway tunnels to Madison Square Garden. There, they locate numerous eggs, having finally found the nest.
As they attempt to destroy them by planting explosives, the eggs suddenly hatch. Sensing the human intruders as food, they begin attacking them. Dr. Tatopoulos, Palotti, Timmonds and Roaché take refuge in the coliseum's broadcast booth and send a live news report to alert the military of what will happen if the lizards escape. A prompt response involving an airstrike is initiated as the four escape moments before the arena is bombed. Godzilla however, survived the torpedo attack earlier underwater and emerges from the venue's ruins. Discovering all of its offspring dead, it roars in anger and chases Dr. Tatopoulos, Roaché, Timmonds and Palotti through the streets of Manhattan.
In pursuit of the quartet, Godzilla eventually makes its way to the Brooklyn Bridge. The creature becomes trapped in its steel suspension cables, making it an easy target. After being successfully struck with missiles by military aircraft, it collapses (smashing the cab under its jaw) and slowly dies. Meanwhile, amidst the Garden's ruins, a lone egg has survived the aerial bombardment and begins to hatch.