Sandra Brody (Juliette Binoche) dies in the beginning of the film as she was sent to the core of a nuclear power plant in Japan by her husband, Joe Brody (Bryan Cranston). This haunts him for the rest of his life. Their son, Ford Brody (Aaron Taylor-Johnson) watches the plant collapse while in school.
Fifteen years later, Ford is an explosive ordnance disposal officer in the United States Navy living in San Francisco. He is married to nurse Elle (Elizabeth Olson) and have a son, Sam (Carson Bolde). Joe is living in Japan trying to figure out what happened that day at the plant. Japan states it was an earthquake and the area is quarantined because of radiation.
Ford goes back to Japan as Joe has been arrested breaching the quarantine area. They soon discover upon returning the power plant that there is no radiation and something is growing in a massive egg. Ishiro Serizawa (Ken Watanabe) and Vivienne Graham (Sally Hawkins), who are on site, have been studying the various creatures linked with this egg. The egg hatches and a MUTO (massive unidentified terrestrial organism) emerges with wings. This destroys the area and eventually kills Joe.
Ishior, Vivienne and Ford are relocated on the aircraft carrier USS Saratoga where the US Navy has a base of operations with Navy Admiral William Stenz (David Strathaim). This MUTO feeds off radiation which is why the area was not contaminated.
The US and the MUTO fight eventually drawing out Godzilla devastating Hawaii in the process. There is another MUTO which was laying dormant in Nevada feeding off the reserve of nuclear waste placed in the desert. This MUTO does not have wings. It is believed they will meet and mate in San Francisco.
Godzilla and both MUTO have a large fight in San Francisco while Ford and the other military personnel go in to disarm a warhead which was sent to lure the MUTO away from the city. Ford destroys the female nest which distracts the female MUTO then Godzilla kills the male MUTO. The female MUTO kills the rest of the military personnel. Ford is able to get the warhead onto the boat out to sea so it doesn’t destroy more city. Godzilla kills the female MUTO and beheads her. Ford is rescued from the boat before the warhead goes off. Godzilla collapse on the shore.
The next day we find that Ford is reunited with his family. Godzilla isn’t dead and swims out to sea.