In 1954, Godzilla, a colossal prehistoric alpha predator, is lured to Bikini Atoll in an attempt to kill him with a nuclear weapon. In 1999, Monarch scientists Ishiro Serizawa and Vivienne Graham investigate the skeleton of a monster similar to Godzilla in a cavern unearthed by a collapsed uranium mine in the Philippines. They find two giant spores, one dormant and one hatched, along with a trail leading to the sea. In Japan, the Janjira Nuclear Power Plant experiences unusual seismic activity. Supervisor Joe Brody sends his wife Sandra to lead a team of technicians into the reactor. A tremor breaches the reactor, forcing Joe to close the reactor door before Sandra and her team can escape while the plant collapses.
In 2014, Joe and Sandra's son Ford, a U.S. Navy EOD officer, returns from a tour of duty to his wife, Elle, and son Sam in San Francisco. He departs for Japan after Joe is detained for trespassing in Janjira's quarantine zone. Joe is determined to find out the cause of the meltdown and persuades Ford to accompany him to retrieve vital data from their old home. They learn that the zone is uncontaminated and retrieve the data, but are discovered and taken to a facility in the plant's ruins. The facility harbors a massive chrysalis that has been feeding off the plant's reactors for fifteen years and emitting intense electromagnetic pulses over time. A giant winged insect-like creature emerges from the chrysalis and escapes, destroying the facility. Joe is severely injured and later dies. The incident is reported publicly as an earthquake.
Serizawa and Graham join a U.S. Navy task force led by Admiral William Stenz to search for the creature, dubbed a "MUTO" (Massive Unidentified Terrestrial Organism). Serizawa and Graham reveal to Ford that a 1954 deep-sea expedition awakened Godzilla. Nuclear tests in the 1950s were attempts to kill him; when this did not work, Project Monarch was established to study Godzilla and similar monsters secretly. They explain that the MUTO caused the Janjira meltdown. Ford reveals Joe had monitored echolocation signals indicating the MUTO was communicating with something, presumably Godzilla.
The MUTO attacks a Russian submarine and drops it in O'ahu to eat its nuclear material. Godzilla arrives, causing a tsunami in Honolulu, and briefly engages the MUTO in battle until it flees. Serizawa deduces Godzilla was only listening and that the MUTO was communicating with something else, prompting the military to investigate the other spore stored in the Yucca Mountain nuclear waste repository in Nevada. A second, bigger, wingless MUTO has emerged and attacks Las Vegas. The scientists deduce that the first MUTO is a male and the second is a female, their signals being a mating call.
Over the scientists' objections, Stenz approves a plan of using nuclear warheads to lure all three monsters out into the open ocean and destroy them. Returning to the U.S., Ford joins the team delivering the warheads by train, but the female MUTO intercepts them and devours most of the warheads. The remaining warhead is airlifted with Ford to San Francisco, where the monsters are converging, and activated after Godzilla appears at the Golden Gate Bridge. The male MUTO snatches the warhead and takes it to the female, who forms a nest around it in the Chinatown area.
While Godzilla and the MUTOs battle, Ford and a strike team enter the city via HALO jump to find and disarm the warhead before it detonates. Unable to access the timer, the team gets the warhead onto a boat for disposal at sea while Ford destroys the nest. Godzilla defeats the MUTOs and collapses from exhaustion. Ford gets the boat out to the open sea, is rescued before the warhead explodes, and reunites with his family at an emergency shelter the following morning. Godzilla reawakens and returns to the sea, while the media dubs him the "King of the Monsters".
Five years after the revelation of giant monsters, called "Titans", Dr. Emma Russell, a paleobiologist working for the Titan-studying organization Monarch, and her daughter Madison witness the birth of a giant larva named Mothra. Emma calms Mothra with the "Orca", a device that emits bioacoustic frequencies to attract Titans or alter their behavior. A group of eco-terrorists, led by former British Army Colonel Alan Jonah, attacks the base and abducts Emma and Madison, while Mothra flees and pupates under a nearby waterfall.
Monarch scientists Dr. Ishirō Serizawa and Vivienne Graham approach former employee Dr. Mark Russell, Emma's ex-husband and Madison's father, to help track them down. Mark is initially reluctant due to his hatred toward Godzilla, whom he blames for his son Andrew's death in San Francisco, but eventually agrees. The Monarch team follows Godzilla to Antarctica, where Jonah plans to free a three-headed Titan codenamed "Monster Zero". Emma frees and awakens Monster Zero, which kills Graham and other members of Monarch's team, battles Godzilla, and flies off. The Monarch team realizes that Emma is working with the terrorists. From a bunker, Emma contacts Monarch, arguing that the Titans must all be awakened to heal Earth from the human impact on the environment, pointing to Monarch research indicating that Titans can terraform and replenish ecosystems using their radiation.
Conflicted, Madison begs her mother to reconsider, but Emma awakens Rodan in Mexico, who is lured toward Monster Zero. Monster Zero defeats Rodan and pursues the Monarch team, but Godzilla ambushes him, severing his left head. During the fight, the U.S. military launches a prototype weapon called the "Oxygen Destroyer", which seemingly kills Godzilla, but does not affect Monster Zero, who regrows his lost head and awakens the other dormant Titans worldwide; Rodan, who survived, submits to his rule. Horrified and disillusioned, Madison disowns Emma.
Through analyzing Monster Zero's abilities and mythological texts, Monarch deduces that he is King Ghidorah, a highly destructive alien who likely seeks to xenoform Earth to his liking. A fully transformed Mothra flies to Monarch's Bermuda base to communicate with Godzilla, who is recuperating in an ancient, radioactive underwater city, which the Monarch team discovers in a nuclear submarine. Deducing that it will take too long for Godzilla to heal on his own, Serizawa sacrifices himself by manually detonating a nuclear warhead next to Godzilla to speed up the process. The explosion destroys Godzilla's lair, but revives him and increases his power.
Emma realizes that Ghidorah's reign over the other Titans is bringing destruction far worse than anything humans could inflict, but Jonah ignores her pleas to try and stop it. Madison overhears her mother's plan to lure Ghidorah to Boston using the Orca, and steals the device to implement it herself. Arriving at Fenway Park, she broadcasts a frequency that calms the Titans, but unwittingly attracts them to her location. Ghidorah, attracted by the frequency, lands in Boston and almost kills Madison, but Godzilla, backed up by Monarch and military forces, arrives to battle him. Mark leads a team to rescue Madison, while learning that Godzilla's radiation levels are still increasing and will lead to a thermonuclear explosion. Mothra arrives to help Godzilla, but she is intercepted by Rodan, whom she defeats despite sustaining injuries.
Ghidorah overpowers Godzilla, but Mothra sacrifices herself and transfers her energy to Godzilla. The Russells are reunited and reactivate the Orca to lure Ghidorah away from Godzilla, buying time for him to recover. Emma stays behind with the Orca to distract Ghidorah, allowing her family and the Monarch team to escape, and is killed. After absorbing Mothra's energy, Godzilla enters a newly empowered state and vaporizes Ghidorah's body with several nuclear pulses, before incinerating Ghidorah's remaining head with his atomic breath. Rodan and several other Titans converge on Godzilla and bow to him.
During the end credits, news clippings and Monarch public files show that the Titans are healing Earth, a suspected second Mothra egg has been discovered, and some Titans are converging on Skull Island. Ancient cave paintings depict Godzilla and a Kong-like Titan locked in battle. In a post-credits scene, Jonah and his forces purchase Ghidorah's decapitated left head in Mexico.
Five years after the three headed dragon-like extraterrestrial, King Ghidorah, awakened giant monsters, known as "Titans", and was defeated by Godzilla, Kong is monitored by Monarch within a giant dome on Skull Island, which has been struck by a perpetual storm. Jia, the last Iwi native and young adopted daughter of Kong expert Ilene Andrews, visits Kong. Jia is deaf and communicates via sign language. Andrews grows concerned that the storm will eventually consume the island, but she dismisses ideas to move Kong to a new home, fearing that Godzilla would come for him once he leaves the island.
Apex Cybernetics employee and Titan conspiracy podcast host Bernie Hayes extracts data suggesting sinister activities at Apex's Pensacola facility. Godzilla suddenly attacks the facility and Bernie stumbles on a massive device emitting a beacon during the rampage. Madison Russell, a listener to Bernie's podcast, enlists her friend Josh Valentine to investigate Godzilla's attacks.
Apex CEO Walter Simmons recruits former Monarch scientist and Hollow Earth theorist Nathan Lind to guide a search for a power source into the Hollow Earth, the Titans' home world. Lind is hesitant as his brother died in a previous expedition to the Hollow Earth due to a strong reverse-gravitational effect. He agrees after Walter reveals that Apex has developed HEAVs (Hollow Earth Anti-gravitational Vehicles), specialized craft able to withstand the gravity field.
Lind convinces Andrews to let Kong guide them via an entrance in Antarctica. Lind, Andrews, and an Apex team led by Walter's daughter Maia board a barge escorted by the US Navy, carrying a sedated and restrained Kong. Godzilla attacks the convoy and defeats Kong, then retreats after the ships trick him into thinking they are destroyed. Kong is airlifted to the Hollow Earth entrance, and the team follows him into the tunnel in the HEAVs.
Bernie joins Madison and Josh in their investigation. They sneak into the wrecked Apex base, discover a secret underground facility, and become locked into a hyperloop transport to Apex's Hong Kong headquarters where they find a test of Mechagodzilla, which is telepathically controlled by Ren Serizawa, the son of the late Ishirō Serizawa, via neural networks from the severed head of Ghidorah. Walter intends to harness the Hollow Earth's energy to overcome Mechagodzilla's power supply limitations.
Inside the Hollow Earth, Kong and the team find an ecosystem similar to Skull Island. In his species' ancestral throne room, they find the remains of an ancient war with Godzilla's kind and a glowing axe made from another of Godzilla's dorsal plates. Identifying the power source, the Apex team sends its signature back to their Hong Kong base despite Andrews' protests. Attracted by Mechagodzilla's activation, Godzilla arrives in Hong Kong and, sensing Kong's presence, blasts a hole through the earth with his atomic breath. After provoking him with gunfire, Maia and the Apex team's HEAV is crushed by Kong. Kong, Andrews, Jia, and Lind ascend to Hong Kong, where Kong engages Godzilla in a final battle. Godzilla emerges victorious, leaving Kong in a bradycardia state.
Madison, Josh, and Bernie are caught by security and taken to Walter, who orders Ren to activate Mechagodzilla. Now possessed by Ghidorah's consciousness, Mechagodzilla kills Walter, electrocutes Ren, attacks Hong Kong, and overpowers Godzilla. Lind revives the dying Kong by detonating the HEAV on his chest, acting like a defibrillator. Jia convinces Kong to help Godzilla, who is nearly killed before Kong saves him. As Mechagodzilla overpowers both Titans, Josh momentarily short-circuits Mechagodzilla's controls with Bernie's liquor. Godzilla charges Kong's axe with his atomic breath, allowing Kong to destroy Mechagodzilla. Madison, Bernie, and Josh reunite with Madison's father, Mark, while Godzilla and Kong acknowledge each other and go their separate ways.
Sometime later, Monarch establishes an observation post in Hollow Earth, where Kong now rules.
Three years after defeating Mechagodzilla, Kong has established his new territory in Hollow Earth and searches for more of his kind. On the Earth's surface, Godzilla continues to maintain order between humanity and giant monsters, known as "Titans"; killing Titanus Scylla for attacking Rome, Italy, and resting in the Colosseum.
A Monarch observation outpost stationed in Hollow Earth picks up an unidentified signal. On the surface, the signal causes Jia, the last known survivor of the Iwi tribe from Skull Island, to experience hallucinations and visions in school, causing her adoptive mother, Kong expert Dr. Ilene Andrews, to worry. Also sensing the signal, Godzilla leaves Rome and attacks a nuclear plant in France to absorb radiation. He then heads to the lair of the Titan Tiamat in the Arctic. Monarch believes Godzilla is strengthening himself for an oncoming threat.
When a sinkhole opens near his home, Kong discovers an uncharted realm where a tribe of his species has survived, including a juvenile ape named Suko. After a brief initial confrontation, Kong convinces Suko to lead him to the tribe's lair and the two slowly bond on their journey. Andrews, Jia, Titan veterinarian Trapper, and conspiracy podcaster Bernie Hayes travel to Hollow Earth to locate the source of the signal and find the Monarch outpost destroyed. As they follow the signal, they discover a temple that leads them to a subterranean section, housing a surviving Iwi tribe, who communicate telepathically with each other and live beneath portals to the surface. Inspecting the temple, they realize that the signal was a telepathic distress call sent by the Iwi. While observing Jia socializing with the Iwi, Andrews voices her fears to Trapper that Jia may choose to stay with her people and that Andrews would have to accept it.
Inside a temple, Andrews uncovers hieroglyphics displaying the past and future: a tyrannical ape titan known as the Skar King once attempted to conquer the surface world and waged war against Godzilla's species, triggering an ice age, but Godzilla defeated him by trapping the Skar King and his tribe deep within Hollow Earth. The prophecy also indicates that Jia is the key to reawakening Mothra. Kong encounters the tribe and confronts the Skar King. After a brief battle, Skar King resorts to summoning his enslaved ice-breathing Titan Shimo, using a crystal that causes her pain and forces her to attack Kong. Shimo's ice breath injures Kong's right arm, causing frostbite. With Suko's help, Kong manages to escape, though he loses his axe in the process. Sensing Jia, Kong locates the temple and is fitted by Trapper with a prototype exoskeletal glove to strengthen and heal his frostbitten arm. Unknown to them, an ape follows them and informs the Skar King that the protective barrier leading to the surface portals has been opened. Jia successfully awakens the reborn Mothra.
Meanwhile, Godzilla kills Tiamat and absorbs cosmic radiation from her lair, which turns his dorsal plates magenta. Hoping to lure Godzilla to Hollow Earth to assist him, Kong surfaces in Cairo and calls out to him. Despite Kong's attempts to communicate, an enraged Godzilla attacks him, and a brief fight ensues until Mothra intervenes and soothes Godzilla. The three Titans return to the Hollow Earth and engage the Skar King's forces in battle. The Skar King and Shimo manage to use one of the portals to escape to the surface, forcing Godzilla and Kong to chase them to Rio de Janeiro, where Shimo induces a second ice age at the Skar King's command. The factions are evenly matched until Suko arrives with Kong's axe and destroys the control crystal. Now free, Shimo turns on the Skar King and freezes him solid, allowing Kong to shatter him to pieces.
After undoing Shimo's ice age with his atomic breath, Godzilla returns to rest in the Colosseum. Jia alleviates Andrews' concerns by choosing to stay with her. Mothra restores the protective barrier of the Iwi's home and the portals. Kong returns with Shimo and Suko to Hollow Earth where he reunites with his tribe and becomes their new leader.
Godzilla x Kong: Supernova is scheduled to be released in the United States by Warner Bros. on March 26, 2027, in IMAX.