Opening credit sequence rolls over archive footage of nuclear tests in the 1950s. Extra information in the opening credits is redacted with strips of white. Nuclear bombs are going off, military personnel are slipping on protective eye-wear, and ominous Godzilla spines briefly emerge from beneath the waves. They are trying to kill Godzilla. It doesn't work and he screams his disapproval.
In 1999 a helicopter bearing the name "Monarch" glides over a huge excavation in the Philippines. It looks like a open pit mine. Thousands of workers labor in the massive trenches. As the 'copter lands, a Japanese researcher named Ichiro Serizawa (Ken Watanabe) and his British assistant Vivienne Graham (Sally Hawkins) emerge. An American supervisor informs them that they had readings that suggested a uranium find. They loaded heavy equipment onto the site, only for it to collapse into an underground cavern. They head there to find the skeletonized carcass of a massive creature, one that fills the cave as far as the eye can see.
Hanging from the cave ceiling appears to be a cocoon of some type, as well as one that looks like it has hatched. Going further into the cave, it looks as though some enormous thing has crawled from the cave and torn a wound across the landscape as it headed toward the sea. Serizawa and Graham puzzle over what could have emerged from the cocoon.
In Japan, at the Janjira nuclear power facility, Joe Brody (Bryan Cranston) is on the phone frantically concerned about local seismic activity. He thinks the power plant should be shut down as a precaution. As an American, he is concerned about ruffling Japanese feathers, but insists on a meeting to air his concerns. His somewhat shy son has made a sign for him. It's his birthday. His wife, Sandy (Juliette Binoche), hustles the son off to school. She reminds Brody that it's his birthday and his son, Ford, had prepared a surprise. They head off to the plant and he tells his wife to head down into the reactor zone to make sure nothing has been damaged by the shaking.
Once at the plant, Brody makes his case. His superiors think the activity is just aftershocks from the recent Philippine "earthquakes." Brody says that the seismic readout on a computer display is unusual & couldn't possibly be just an earthquake. One of his assistants tells him that the increase in seismic rumblings has been recorded in hours, not days. Suddenly, a major tremor hits the plant. Brody yells: "We need to shut down now!" Before the process can even begin, another shaker rocks the plant, triggering red lights all over the place. The reactor has been breached and Brody's wife is down there.
Brody races downstairs, demanding that the protective shield door be kept on manual override so he can save his wife. Sandy and her team run full tilt trying to stay ahead of a radioactive cloud rushing through the tunnels that will kill them despite their protective suits. They are making good time until a teammate stumbles and Sandy stops to assist him.
Meanwhile, Brody has arrived at the door and confirmed that he has control. He gets a walkie talkie message that Sandy is done for. Brody is overcome with emotion, literally shaking at the prospect of losing her. She tells him that he needs to shut the door to save the city. He waits until the last possible moment, then seals the door and their fates. Literally seconds after the primary door has been sealed, Sandy appears with several of her team. Brody weeps as he watches his wife being bathed in the toxic radioactive mist as the secondary door closes.
At his school, little Ford Brody (CJ Adams) witnesses the plant's cooling towers collapsing as he's being evacuated. He knows that his parents work there. All his classmates flee outside while he watches his entire life collapse into ruin.
In the present day, an adult Lt. Ford Brody (Aaron Taylor-Johnson) is returning home after 14 months at sea in the US Navy to his wife Elle (Elizabeth Olsen) and their young son Sam (Carson Bolde) in San Francisco. There's a sweet 'Welcome Home' scene and Ford prepares for some long overdue mommy/daddy time when the phone rings. Ford learns from someone on the line that his estranged father, Joe Brody, has been arrested in Japan for trespassing and is being held by the police. Ford leaves to meet his father.
In Tokyo Ford is obviously disappointed at having to bail out his dad. Joe suffered a nervous breakdown after the accident and their relationship is clearly strained. Joe's small apartment looks like a conspiracy theorist's paradise. Pictures and articles paper the walls. Stacks of books and research are everywhere. Clearly his dad has become obsessed with the accident at Janjira. He's mumbling about echolocation and earthquakes "talking to each other." Out of pity, Ford suggests that his dad come home with him. Joe hasn't seen his grandson in years and desperately needs a break. Joe, however, is adamant about continuing his investigation: he needs to know what happened that day. His wife is still buried in the rubble of the "quarantine zone." He mentions that he needs to get back to his house to retrieve his research and sadly shares that he doesn't even have a picture of his wife to cherish.
Begrudgingly, Ford decides to help his dad. They head back to the old neighborhood, which looks abandoned and overrun. Suddenly, a pack of dogs gambols through the scene. How could that happen in a radioactive wasteland? Joe checks his Geiger counter which shows no radiation at all. Impulsively, he snatches off his protective headgear and breathes deeply, proving the air is completely safe. Ford is becoming convinced that something is amiss here. They rummage through the house and Joe grabs his 3.5 inch ZIP discs. He finds a picture of Sandy and turns to see Ford's birthday sign, still strung up after all these years. Meanwhile, Ford finds an old army toy soldier that he pockets.
The beating of helicopter blades shakes them from their reverie. As they head outside, they're immediately scooped up by Japanese-speaking security guards and driven to the "abandoned" nuclear plant. Serizawa and Graham are talking with some others. They are concerned about activity surrounding an odd cone-shaped organic structure protruding from the surface of the old reactor. Someone interrupts them to say they need to come with him. They are taken to where Joe is being interrogated. He comes across as manic and a little loopy, but Graham confirms that his data is strikingly similar to what they're seeing now. He's the only one left who knows what happened 15 years ago and demands to see his son and get answers regarding the disaster that killed his wife.
Back in the main room, the readings confirm that EMP pulses are knocking out their electronics with alarming frequency... just like in 1999. Serizawa concedes that it's time to kill the program. A steel containment net is lowered and millions of watts of electricity are applied to the chrysalis -- the massive jolt of electricity appears to destroy the organic pod and the light that pulsated in it dies out. Suddenly, a massive multi-legged creature cracks out of the shell and pounds its clawed leg on the ground, creating an EMP pulse that kills all power in the facility. People are screaming and running as the creature strains against its enclosure. Meanwhile Joe is still handcuffed in a security vehicle. He watches helplessly as people are slaughtered around him. Suddenly, a support smashes the detainment vehicle he was trapped in and he's free. Joe watches in horror from an elevated walkway as his son faces death. But his own safety is in jeopardy as the bridge is demolished and he tumbles in a horrible fall. Ford dons a gas mask and looks up just in time to see the creature unfurl giant wings and fly off.
The next day, Captain Russell Hampton (Richard T. Jones) informs Serizawa that the U.S. military is taking over. He asks Serizawa who he needs on his team. He points to Joe, bandaged and on a stretcher. They take Joe and Ford in a military transport. Unfortunately, Joe doesn't survive for long. Serizawa and the others turn to Ford, asking him if he knows anything about his father's findings. Ford is reluctant to comment on his father's obsessive behavior but remembers something about echolocation. Serizawa clues into this, brings Ford into a briefing room, and explains to Ford that the recently hatched "MUTO" (Massive Unidentified Terrestrial Organism) may be trying to communicate with another giant monster that was found roaming the Pacific a long long time ago. Serizawa then presents the same vintage nuclear test footage from 1954 that we see in the opening credits, but with a few crucial details included, mainly a few frames of a familiar giant spiny creature. Serizawa explains that the nuclear tests weren't tests; they were attempts to kill this creature. This creature had been named "Godzilla", and Serizawa is convinced he is returning, a feeling that is soon confirmed when he is spotted soon thereafter. The naval fleet follows Godzilla. Meanwhile, Elle freaks out about the news coverage of the Japan damage and can't reach Ford.
Since Ford doesn't have much to offer, he's put on a helicopter headed to Hawaii for a flight back home. The Navy confirms that the MUTO is headed across the Pacific. The fleet heads in that direction, flanking Godzilla's spines, which are heading in the same direction. Serizawa posits that Godzilla is tracking the MUTO and wants to fight it to restore balance to nature.
In Honolulu, Ford is at the airport, waiting for the train to his terminal. He's playing with the toy solider and a little Japanese boy becomes fascinated with it. As the boy wanders onto the train without his parents and the doors close. They freak out, but Ford mouths that he will being their boy back. He hopes that he won't miss his flight.
Back to the carrier ship, they've heard that the Russians are missing a nuclear sub. The MUTO eats radiation (which is why the nuclear plant was free of toxic waste). It may have taken the sub as a meal. They send a team into the forest near Honolulu to investigate. The team finds the sub, covered in gooey slime and stuck in a tree. The MUTO is snacking on nuclear fuel canisters. An airborne attack is launched, but the MUTO fires its EMP, knocking out all navigation controls for the jets and sending them plummeting to earth. At the airport, power is knocked out, including power to the train at the airport. Ford doesn't realize that the MUTO has caused the outage and assures the little boy that the power will come back soon.
At a hotel luau, a little girl sees the explosion of the planes in the far-off hills. The crowd is becoming worried as the little girl notices that the sea water seems to be receding from the shore at a rapid pace. Something is displacing an immense amount of water.
Very quickly, we see that the thing moving all that water is Godzilla. Honolulu is flooded as the beast reaches ground. The luau (and everything else downtown) are flooded. At the airport, power is restored, but reveals the MUTO has reached the elevated tracks and the train is headed straight into its jaws. The behemoth shreds the track, sending passengers to their doom. Ford barely hangs on, grabbing the kid before he slides out of the mangled train. Godzilla squares off against the MUTO, but it manages to escape, flapping its giant wings and continuing its journey to the mainland.
Back in San Francisco, Elle is asking her son to go to bed as he watches the developing destruction on the news. The whole world now knows that the MUTO and Godzilla exist.
Back on the ship, they're tracking the MUTO's path. Looks like it's headed to San Francisco. Graham and Serizawa realize that it must be headed to the other MUTO, long-thought dead. Unfortunately, the dangerously radioactive body has been stored in the midst of an unlimited food supply: the Yucca Mountain nuclear waste facility in Nevada. Troops arrive to discover that the MUTO, now confirmed as a female, has escaped and is making a path to meet her mate. The path leads directly through Las Vegas. The second MUTO is much larger and more powerful than the first and lumbers straight through Las Vegas, destroying whatever lies in it's path.
The Navy has hatched a plan to lure the two MUTOs off shore with a nuclear missile. Godzilla will be close behind. Then they'll detonate the bomb, wiping out all three monsters. Graham is amazed at the short-sightedness of the plan. Because the MUTOs eat radiation, she and Serizawa believe the plan won't work. Captain Hampton claims that nothing can survive the power of the newer bombs. Serizawa isn't convinced.
Meanwhile, after delivering the boy to his parents in devastated Honolulu, Ford hops onto a Navy transport headed to the mainland. A train is being prepared to transport the two weapons (the bait and the killer bomb). Ford shoehorns himself into the detail, citing his expertise in ordnance handling. The bombs will be transported by train to the coast where the plan will be set into motion. Things seems to be going just fine until a tremor stops the train right before a treacherous mountain bridge. The team attempts to radio ahead, but the screams over the walkie don't bring good news. Uncertain if the bridge is even there, they break into two groups. It looks OK at first, but the female MUTO has been lying in wait. It smashes the bridge, gobbles down one of the nukes, and kills everybody on the train (except for Ford, who jumps into the river just as the bridge is shattered).
By morning, a recovery team has found Ford and the nuke. They'll fly the remaining bomb and try to make do with a modification of the initial idea. The President approves. Serizawa comments on the arrogance of man (thinking that we can control nature when it's the other way around).
The two MUTOs are headed for their reunion in San Francisco, with Godzilla in close pursuit. The Navy has been tacitly tolerating the monster as it has expressed no direct threat to the ships, but they are committed to destroying them all despite Serizawa's protests. Ford has called Elle at the hospital to assure her he's on his way, and asks her to please wait for him. Meanwhile, the whole city is prepping for an emergency evacuation. Elle wants to keep her son with her, but relents, trusting his care to a co-worker. Evacuation buses are stalled on the Golden Gate bridge as troops in tanks position themselves against the kaiju threat.
The Navy has rigged the bomb with an analog countdown timer (to avoid being disabled by MUTO's EMP). They set the clock when a winged MUTO attacks. He's looking for a snack for his mate and delivers the bomb to her. The larger MUTO tears up part of Chinatown make a nest for their offspring; the nuke will offer nutrition until they hatch. Godzilla, sensing his prey, emerges from the depths right by the Golden Gate Bridge. The troops attack instinctively, inciting Godzilla to tear through the bridge. The bus driver sees his chance and barrels through barricades to take his charges to safety.
Ford, though injured, claims he can disarm the trigger in about 60 seconds. He's on the team for a risky HALO jump into San Francisco to grab the bomb, defuse it, and make one last try to blow the monsters to smithereens.
They make the jump, only losing a couple of guys when Godzilla shows up ready to fight the monsters. Godzilla is doing pretty well against the smaller, winged male, but when the big female leaves the nest to help, they join up to attack Godzilla. The troops have found the nest and the nuke, but the the casing is damaged and they can't disarm it there. They begin to move it to a boat where they have more tools and can send it away from the city...
The fight between the giants continues in the city where the MUTOs are ruthlessly jabbing their hooks into Godzilla's massive body. He looks done for but continues to fight them.
Back at the nest, Ford sees thousands of eggs and realizes they're an even bigger threat. Lagging behind, he pops off the covers on spoutsfrom a destroyed tanker truck to flood the chamber with gasoline.
Godzilla's fight with the MUTOs seems to be turning to his enemies' advantage: he's been mangled by the MUTOs, when suddenly the nest explodes, destroying all the eggs and sending the female screaming back to the nest in a panic. This is just the break Godzilla needs. He gets his second wind and re-engages with the flying MUTO. Air superiority appears to give MUTO an edge, but Godzilla's long spiked tail knocks the MUTO into a building, killing it.
Meanwhile, Ford has been caught in the aftershock of the explosion. The female MUTO grieves the loss of the babies, but smells the nuke and heads back to grab it. The female seems to notice Ford and leans menacingly close to him when Godzilla suddenly reappears and his spinal crest begins to glow blue. The beast lets loose with an enormous blast of radiation breath at the female MUTO, driving it back. He continues to fight it hand-to-hand.
The team reaches the ship and tries to make for open water, but an EMP from the female MUTO kills the engines. The troops valiantly try to save the mission, but the beast arrives and starts ripping them to shreds. As the monster turns to attack some troops on shore, Ford goes to the boat to disarm the bomb. The casing is too far gone and the female MUTO sets her sights on his tiny vessel. Suddenly, Godzilla stealthily sneaks and grabs mama MUTO by the throat. Ripping her jaws open, he fires an atomic fire blast down her throat, incinerating the beast and tearing her head off. Finally, Godzilla succumbs to its injuries and collapses on the shore.
Meanwhile the ship's power sputters back to life and Ford directs the GPS to take the ship into the bay. There's no time to disarm it now. He falls to the deck, seemingly accepting of his fate. A blinking light draws him back into consciousness as a med-evac helicopter lifts him to safety. In the distance, the auto-piloted boat erupts into an nuclear explosion, safely away from the city.
In the aftermath, the badly-injured corpse of Godzilla lies in the streets of San Francisco. Ford is limping through a hastily converted stadium shelter. He has found his son, but emergency teams are still attempting to rescue folks from the hospital that was demolished in the kaiju battle, and Elle is still missing. Suddenly, son sees Elle and she sees Ford and they hug... reunited and threat averted.
Meanwhile, Serizawa looks with regret on the still body of the great beast. Suddenly, it snorts into motion, slowly righting itself and lumbering through the streets toward the water. Serizawa smiles, happy that this mighty force of nature has survived. News reports announce that the "King of Monsters Saved the City!" Godzilla then dives back into the water and swims away into the ocean.