Five years after Godzilla defeated King Ghidorah, Kong is monitored by Monarch within a giant dome on Skull Island. Kong is visited by Jia, the last Iwi native and Kong expert Ilene Andrews' adopted daughter, who is deaf and communicates with Kong via sign language.
Bernie Hayes, an employee of Apex Cybernetics and host of a Titan conspiracy theory podcast, extracts data suggesting sinister activities at a Pensacola facility. However, Godzilla suddenly attacks the facility; during the rampage, Bernie stumbles on a massive device. Madison Russell, a fan of Bernie's podcast, enlists her friend Josh to investigate Godzilla's attacks. Apex CEO Walter Simmons recruits Nathan Lind, a Hollow Earth theorist, to guide a search for a power source into the Hollow Earth, the homeworld of the Titans. Nathan is initially hesitant as his brother died on an expedition to Hollow Earth due to a strong reverse-gravitational effect. He agrees after Walter reveals that Apex has developed HEAVs, specialized crafts able to withstand the pressure exerted by the gravity field.
Nathan meets with Ilene and convinces her to let Kong guide them through the Hollow Earth via an outpost in Antarctica. Nathan, Ilene, and an Apex team led by Walter's daughter Maia board a modified barge escorted by the U. S. Navy that carries a sedated and restrained Kong. Godzilla attacks the convoy and defeats Kong, but retreats after the ships disable their power and trick him into thinking they are destroyed. To avoid alerting Godzilla, Kong is airlifted to the Hollow Earth entrance, and Jia convinces him to enter the tunnel while the team follows him in the HEAVs.
Madison and Josh find Bernie, who joins their investigation. They sneak into the wrecked Apex base, discover a secret facility underground, and are inadvertently locked into an underground monorail transport to an Apex facility in Hong Kong, where they unwittingly stumble on a test of Mechagodzilla. It is telepathically controlled by Ren Serizawa, the son of the late Ishiro Serizawa, through the neural networks from a severed head of Ghidorah, but is hobbled by its power supply's limitations. Walter intends to harness the Hollow Earth's energy to overcome Mechagodzilla's limitations.
Inside the Hollow Earth, Kong and the team find an ecosystem similar to Skull Island. They discover his species' ancestral throne room, where they find remains of an ancient war with Godzilla's kind and a glowing axe made from another Godzilla's dorsal plates. As they find the power source, the Apex team sends its signature back to their Hong Kong base despite Ilene's protests. Attracted by Mechagodzilla's activation, Godzilla arrives in Hong Kong, and sensing Kong, he directly drills a shaft to the throne room with his atomic breath. In the ensuing mayhem, Maia and the Apex team attempt to escape but their HEAV is crushed by Kong. Kong, Ilene, Jia, and Nathan ascend to Hong Kong, where Godzilla and Kong battle. Godzilla is initially overpowered by Kong, but Godzilla emerges victorious while Kong loses consciousness.
Madison, Josh, and Bernie are caught by security and taken to Walter. Despite Ren's concerns over the power source's volatility, Walter orders him to activate Mechagodzilla. They lose control of Mechagodzilla, who kills Walter and electrocutes Ren, and then attacks Hong Kong. Godzilla and Mechagodzilla battle, but Godzilla is overwhelmed. Nathan revives Kong by destroying the HEAV, and Jia convinces him to help Godzilla. As Mechagodzilla overpowers both Titans, Josh short-circuits Mechagodzilla's controls with Bernie's flask of liquor, momentarily interrupting the mech. Godzilla supercharges Kong's axe with his atomic breath, allowing Kong to destroy Mechagodzilla. Madison, Bernie, and Josh reunite with Mark Russell, while Godzilla and Kong acknowledge each other before the two go their separate ways. Sometime later, Monarch has established an observation post in the Hollow Earth, where Kong now rules.