Cut to 1999...
A Monarch helicopter (we saw their name in the credit sequence) glides over a HUGE excavation in the Philippines. It looks like a 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 GIANT creature. It 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? What could it be? 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.
In Japan, Joe Brody (Bryan Cranston) is on the phone frantically concerned about seismic activity. He thinks the nuclear power plant he works for 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 the wife to head down into the reactor zone to make sure nothing has been damaged in the shaking.
Once at the plant, Brody makes his case. His superiors think the activity is just aftershocks from the recent Philippines "earthquakes;" Brody says 'no'. 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 the cloud that will doom them. They are making good time until a teammate stumbles and Sandy stops to assist him. OMG, the cloud is right behind them.
Meanwhile, Brody has arrived at the door and confirmed that he has control. Upstairs is freaking out. 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. But there's one more cruel twist of the knife Literally, seconds after the 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.
At his school, little Ford Brody (CJ Adams) observes the plant's cooling towers collapse. He knows that his parents work there. All his classmates flee outside while watches his entire life collapse into ruin.
The 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). 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 other line that his estranged father, Joe Brody, has been arrested in Japan for trespassing and is being held. Ford has to go get him. Looks like Daddy has to break a promise to his son to "be there in the morning."
In Tokyo, Japan, Ford is obviously a little disgusted 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 dad has gone round the bend. 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. He needs a break. Joe, however, is adamant. He needs to know what happened that day. His wife is still buried in the rubble of the "quarantine zone." If he could JUST get back to his house to retrieve his research! He doesn't even have a picture of Sandy 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 gambles 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. It's completely safe. Ford is becoming convinced. Something is amiss here. They rummage through the house and Joe grabs his 3.5 inch floppy 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 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!
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 except that it doesn't work at ALL. Suddenly, a massive multi-legged creature cracks out of the shell and pounds it's clawed leg on the ground creating an EMP pulse that de-powers the facility. People 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 his vehicle 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 he bridge is demolished and he tumbles in a horrible fall. The creature has escaped and lumbered of into the night.
The next day, Captain Russell Hampton (Richard T. Jones) informs Serizawa that the U.S. military is taking over. He asks who does Serizawa need 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. Now all eyes are on Ford. What could he possibly remember from his conversations with his dad? Ford is ashamed to admit that he thought his dad was nuts, but then remembers something about echolocation Serizawa clues into this discovery and brings Ford into a briefing room and explains to Ford that the recently hatched MUTO may be trying to communicate with another giant monster that was found roaming the Pacific a long long time ago. Serizawa then loads up the same vintage nuclear test footage from 1954 that we see in the opening credits, but 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 has been named GODZILLA, and Serizawa is convinced he is returning, a feeling that is soon confirmed when he spotted soon thereafter. The naval fleet follows Godzilla. Meanwhile, Elle is freaked 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 helo headed to Hawai'i for a flight back home. The Navy confirms that the "MUTO" Massive Unidentified Terrestrial Organism is headed across the Pacific. The fleet heads in that direction, flanking Godzilla's spines which is heading in that same direction. Sirezawa 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 on the train to his terminal. He's playing with the toy solider and a little Japanese boy becomes fascinated by it. As the boy wanders onto the train, the doors close. His parents aren't on it with him. They freak out, but Ford mouths that he will being the kid 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 snack. They send a team into the forest near Honolulu to investigate. The team finds the sub, covered in goopy slime and mounted in a tree. The MUTO is snacking on nuclear fuel canisters. An airborne attack is launched, but the MUTO fires off its EMP, knocking out all navigation controls for the jets and sending them plummeting to earth. At the airport, power is knocked out, including to the train. 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 a LOT 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) is toast. At the airport, power is restored, but reveals the MUTO RIGHT OVER THE TRAIN TRACKS. The train is headed straight into its Jaws. The behemoth shreds the track sending passengers to their doom. Ford barely hangs on, but grabs 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 attempting to put her kid to sleep, while he watches the developing destruction on the news. The whole world now knows, the MUTO and Godzilla exists.
Back on the ship, they're tracking the MUTO's path. Looks like he's headed to San Francisco. Graham and Serizawa realize that it must be headed to the other MUTO, long-thought dead Unfortunately, for us, they stored the dangerously radioactive body 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 pregnant female has escaped and is making a path to meet its mate. A path that leads directly through Las Vegas. It doesn't take long for this even BIGGER monster to lay Sin City to utter waste.
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. The MUTOs EAT RADIATION!!! 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 prepped to transport the two weapons (the bait and the killer bomb). Ford shoehorns himself onto 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 up into two groups. It looks OK at first, but the mama MUTO has been laying in wait. It smashes the bridge, gobbles down one of the nukes and kills everybody on the train (except for Ford), who jumped into the river just as the bridge was shattered.
By morning, a recovery team has scooped him and the nuke. They'll fly the remaining bomb and try to make do with a modification of the initial idea. The President gives the thumbs up. Sirezawa comments on the arrogance of man thinking that we can control nature. Actually, it's the other way around.
The two MUTOs are headed for their reunion in Fresco 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 Sirezawa's protests. Ford has called Elle at the hospital to assure her he's on his way. 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. Those evac busses are stalled on the Golden Gate bridge as troops in tanks position themselves against the kaiju threat.
The Navy has prepped the bomb with an an along countdown timer (to avoid being disabled by the MUTO's EMP). They set the clock when winged MUTO attacks. He's looking for a snack for his baby mama and delivers the bomb to her. They tear up some downtown real estate to make a nest for all those little MUTO babies. The nuke is going to offer nutrition until they hatch. Now the bomb is in the midst of downtown, traffic is a FUBAR and hundreds of thousand peoples are at risk. Godzilla, sensing his prey, emerges from the depths right by the bridge. The troops attack instinctively, inciting Godzilla to horribly damage it. The bus driver sees his shot 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 Frisco, to grab the bomb, defuse it and make one last try and blowing the monsters to smithereens.
They make the jump, only losing a couple of guys when Godzilla shows up ready to kick some MUTO butt. Godzilla is doing pretty well against the smaller, winged male, but when big female leaves the nest to help, they tag team him something awful. 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..
Cut back to the monster mash where the MUTOs are ruthlessly jabbing their hooks into every part of GZ's massive body. He looks done for, but slowly rises with telltale blue shimmer of his back scales indicating his trademark blue atomic breath. He blasts the female MUTO with his blue-flame fire breath before being tackled by the male creature.
Back to the nest, Ford sees the thousands of eggs and realizes they're an even bigger threat. Lagging behind, he pops off a fuel switch and floods the chamber with gasoline from a destroyed tanker truck.
Back to monsters it looks like this is the end for Godzilla. He's been mangled by the MUTOs, when suddenly the nest EXPLODES killing 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 and edge, but Godzilla's wicked spiked tail knocks the MUTO into a building, killing it for good.
Meanwhile, Ford was 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. Ford is on his way too. The team reaches the ship and tries to make for open water, but an EMP by 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 gets 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 tears through a building and grabs mama MUTO by the throat. Ripping her jaws open, he fires an atomic fire blast right down her throat, incinerating the beast and tearing its 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 and he falls to the deck seemingly accepting of his fate. A blinking light draws him back into consciousness as a medevac 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 damaged 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 which was demolished in the kaiju battle and Elle is still missing. Suddenly, son sees Elle and she sees Ford and they hug... reunited and the 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. Sirezawa 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.