Five years after Godzilla triumphed over King Ghidorah, Kong finds himself observed by Monarch within a colossal dome situated on Skull Island. Amongst his visitors is Jia (Kaylee Hottle), the last surviving Iwi native and the adopted daughter of Kong's expert, Ilene Andrews (Rebecca Hall), who is also deaf. Jia uses sign language to communicate with Kong, who is growing too large for the electronic confines of the dome. Ilene realizes that Kong cannot remain there for much longer, but she is aware that if he escapes the island, Godzilla will inevitably come after him, as there cannot be two alphas in this world.
In the midst of these developments, Bernie Hayes (Brian Tyree Henry), an employee at Apex Cybernetics and host of a podcast focused on Titan conspiracy theories, uncovers alarming data regarding activities at a facility in Pensacola. The information points to ominous shipments bound for Apex's Hong Kong site, alongside blueprints of a massive machine. Just then, Godzilla unleashes an attack on the facility, during which Bernie stumbles upon a substantial device.
Meanwhile, Madison Russell (Millie Bobby Brown), who is a fan of Bernie's podcast and the daughter of Monarch scientists Mark and the late Emma Russell, theorizes that there exists a motive behind Godzilla's unpredictable behavior, suspecting that Apex could be behind it. She enlists her friend Josh (Julian Dennison) to delve deeper into the mystery behind Godzilla's strikes.
At the helm of Apex is Walter Simmons (Demián Bichir), also the father of Maia (Eiza González), who is leading the tech firm’s initiative to manage the "Titan problem". Walter surreptitiously builds Mechagodzilla to wipe out the Titans. He recruits Nathan Lind (Alexander Skarsgård), a geologist from Monarch who has a history of working alongside Kong, to navigate an expedition into the Hollow Earth, the Titans' original habitat. Walter tries to persuade Nathan that a new energy source is crucial for managing the Titans.
Though Nathan is initially reluctant due to a past expedition that resulted in his brother's death from reverse gravitational forces, he relents when Walter introduces him to the HEAVs (Hollow Earth Aerial Vehicles), which are designed to withstand the pressures of the Hollow Earth. Nathan subsequently partners with Ilene to transport Kong through Antarctica, knowing that only a Titan can unlock the route into the Hollow Earth.
As they set off on a modified barge secured by the U.S. Navy, Kong is sedated and restrained, under the watchful eye of Jia, who astonishes Ilene with her ability to communicate with the Titan. However, chaos ensues when Godzilla attacks the convoy, severely challenging Kong. With the barge in peril, Nathan sets Kong free, and a fierce struggle transpires on an aircraft carrier where Godzilla's atomic breath wreaks havoc, forcing Kong to flee underwater.
In the meantime, Madison and Josh trace Bernie to join him in their investigation. They infiltrate the wreckage of the Apex base, stumble upon a concealed underground monorail, and find themselves inadvertently captured while discovering the facility testing out Mechagodzilla. It becomes evident that Mechagodzilla is remotely controlled by Ren Serizawa (Shun Oguri), the late Ishiro Serizawa's son, but struggles due to power constraints.
As the Apex crew ventures into the Hollow Earth, Kong encounters a familiar yet distinct ecosystem. They discover a throne room that hints at an ancient conflict with Godzilla's kind, along with a mystical ax believed to harness great power. While the Apex team sends signals back to their Hong Kong headquarters, Godzilla is attracted by Mechagodzilla's activation and drills a path to the throne room, where chaos unfolds.
In the ensuing turmoil, Kong and Godzilla collide in an intense showdown in Hong Kong. Initially, Kong gains the advantage but soon finds himself overpowered by Godzilla, leaving him injured and defeated. Meanwhile, Madison, Josh, and Bernie find themselves confronting Walter, who dismisses Ren's apprehensions and commands the activation of Mechagodzilla. Now governed by the malevolent spirit of Ghidorah, Mechagodzilla turns on its creators, annihilating Walter and rampaging through the city.
As Mechagodzilla gains momentum in its fight against Godzilla, Nathan manages to revive Kong, utilizing an electromagnetic pulse to stimulate his heartbeat, aided by Jia's encouragement. In a final act of unity, Josh manages to disrupt Mechagodzilla's control, allowing Godzilla to charge Kong's ax with his atomic breath. Together, they vanquish this technological monster.
After the dust settles, the Titans acknowledge one another before parting ways. Eventually, Monarch establishes an observation base deep within the Hollow Earth, where Kong reigns supreme.
