The film follows the uneasy alliance between Godzilla and Kong as they face a hidden, colossal threat from within Hollow Earth. After establishing his own territory there, Kong discovers a subterranean cavern containing a tribe of his surviving relatives, including a young, orphaned ape named Suko. They are all enslaved by the film’s primary antagonist, the Skar King—a despotic, withered ape who controls an ice-powered Titan named Shimo.

In the Iwi's subterranean kingdom, a massive battle ensues. Shimo freezes parts of the landscape, but Jia manages to break the Skar King's psychic hold over her. Shimo turns on the Skar King. Godzilla and Kong work together; Godzilla fires his atomic breath while Kong delivers the final blow, shattering the Skar King into pieces using the B.E.A.S.T. Glove.

In the aftermath, Godzilla returns to the surface to rest in Rome, while Kong and Shimo return to the Hollow Earth to rule and protect the ape tribe.