On Skull Island, Kong, the mighty ape, is contained within a giant dome by Monarch, the secret scientific organization, to protect him from Godzilla, who has surfaced unpredictably, attacking human cities. Dr. Ilene Andrews, a Monarch anthropologist, acts as Kong's caretaker, observing a deep bond between Kong and a young, orphaned girl named Jia, the only survivor of the island's native tribe, who communicates with Kong through sign language. Elsewhere, Madison Russell, a teenager with a personal stake in the titans, suspects that the provocative behavior of Godzilla is not unprovoked, prompting her to investigate with her friend Josh and a conspiracy theorist podcaster, Bernie Hayes.

Meanwhile, the Apex Cybernetics corporation recruits Dr. Nathan Lind, a former Monarch scientist and Hollow Earth theorist, to lead an expedition into the Hollow Earth, theorized as the ancestral home of the titans. The mission is to harness a powerful energy source believed to reside there, with Kong as their guide. The fragile truce between humans and titans begins to unravel as Apex's true intentions come to light and Godzilla's rampages continue. As Kong is transported from his artificial habitat to the Hollow Earth entry point, his protective human companions realize that their path is on a collision course with Godzilla, leading to a series of dramatic encounters between the two behemoths as they stake their claim as the apex predators of the world.