Godzilla is The film's opening credits play over a montage of French nuclear tests in French Polynesia. A lizard nest is irradiated by the fallout.
A Japanese fishing ship is suddenly attacked by an unseen, giant creature. Only one sailor survives. Traumatized, he is questioned by a mysterious Frenchman (Jean Reno) in a hospital. His only reply is "Gojira."
Dr. Niko Tatopoulos (Matthew Broderick), an NRC scientist, located in the Chernobyl Exclusion Zone researching the effects of radiation on wildlife, is interrupted by the arrival of an agent of the U.S. State Department. He is sent to Panama, escorted by the military, to observe the wreckage of the recovered Japanese fishing ship and a set of massive footprints in the grassy soil. The Frenchman is also there, observing the scene and introduces himself as an insurance agent. Aboard a military aircraft, Nick identifies skin samples he discovered as belonging to an unknown animal. He dismisses the military's theory that the creature is a dinosaur, theorizing that its origins in French Polynesia make it a mutant created by nuclear testing.
Godzilla (as mispronounced by the media) travels to Manhattan and creates havoc in the city, then disappears. The city is evacuated as the military attempt to destroy him. With Nick's help, they set up a fish trap to lure Godzilla out into the open.
He takes the bait, but is scared off by small arms fire and retaliates by breathing strong gusts of combustible wind. After the battle, Nick collects a blood sample. With the help of his ex-girlfriend reporter Audrey Timmonds (Maria Pitillo), he learns that Godzilla reproduces asexually and is collecting food for his offspring.
Audrey then discovers a classified tape concerning the origins of Godzilla. She plans to make a report of it, but her boss Charles Caiman (Harry Shearer) made off with it first. The tape plays on television and the military is outraged. Nick is thrown off the team and kidnapped by the Frenchman who reveals himself to be Agent Philippe Roache of the DGSE.
He and his team have been keeping close watch on events and are planning to cover up the mess they've done regarding the nuclear accident. Suspecting of a nest somewhere in the city, they cooperated with Nick in finding and destroying it.
The military lures Godzilla out again, trying to trap him in the open ground of Central Park, but fails when he sprints off. Godzilla then dives into the waters of the Hudson, where he is attacked by three U.S. Navy nuclear submarines and is seemingly killed.
Nick and Philippe's special ops team, surreptitiously followed by Audrey and her cameraman Victor "Animal" Palotti (Hank Azaria), track through the subway tunnels to Madison Square Garden, where they find over 200 eggs. While the team plants explosives, the eggs begin to hatch and the baby Godzillas begin to feed on the fish left for them. When the fish run out, they begin hunting the team.
After failing to contain the babies and losing several members of the team, Nick, Philippe, Animal and Audrey take refuge in a TV broadcast booth. Believing that the babies will eventually force humanity into extinction if they escape, Nick, Audrey and Animal alert the authorities, who order an immediate strike by a trio of F/A-18 Hornets. The four escape just before the building is destroyed, and the babies are burned to death.
Seconds later, Godzilla, still alive, emerges from the wreckage and witnesses the slaughter of his entire brood. Enraged, he chases the four humans around Manhattan. They manage to alert the military, who advised them to lure Godzilla out into the open (i.e., the Brooklyn Bridge), where he becomes helplessly trapped in the steel suspension cables and is an easy target for the returning fighter planes. Godzilla is then hit mercilessly by missiles, whereupon he falls to the ground and slowly dies.
The crowd and the military celebrate Godzilla's demise. As Nick, Audrey and Animal reconcile, Philippe quietly leaves, taking the videotape Animal had recorded. The film ends in the smoking ruins of Madison Square Garden, and it is revealed a single egg has survived the bombing. Suddenly, the egg begins to crack, and a baby Godzilla hatches and roars.