Three years after defeating Mechagodzilla, Kong has established his new territory in the Hollow Earth and is searching for more of his kind. On Earth’s surface, Godzilla continues to maintain order between humanity and giant monsters, known as “Titans.” He kills Titanus Scylla in Rome and rests in the Colosseum afterward.
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, worrying her adoptive mother and Kong expert, Dr. Ilene Andrews. 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 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. The tribe’s tyrannical leader, Skar King, battles Kong with the aid of an ancient ice-powered Titan, Shimo, whom he controls using a crystal that can cause her pain. Shimo’s ice breath injures Kong’s right arm, causing frostbite, but with Suko’s help, Kong manages to escape after losing his axe.
Andrews and Jia, alongside Titan veterinarian Trapper and conspiracy podcaster Bernie Hayes, travel to Hollow Earth to locate the source of the signal. They find the Monarch outpost destroyed. As the group follows the signal, they discover a temple that leads them to a subterranean section that houses a surviving Iwi tribe, who communicate telepathically with each other, living beneath portals to the surface. Inspecting the temple, they surmise 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: Skar King once attempted to conquer the surface world, forced Shimo to trigger an ice age, and waged war against Godzilla’s species. Godzilla defeated him by trapping him and his tribe deep within Hollow Earth. The prophecy also indicates that Jia would be the key to reawakening Mothra. Sensing Jia, Kong locates the temple and is fitted by Trapper with a prototype exoskeletal glove to strengthen and heal his frostbitten limb. Unknown to them, another 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 Godzilla. Despite Kong’s attempts to communicate, an enraged Godzilla attacks him, and a brief fight ensues until Mothra intervenes. Godzilla, Kong, and Mothra return to the Hollow Earth and engage Skar King and Shimo in battle, during which Kong loses his axe. 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 Skar King’s command. The factions are evenly matched until Suko arrives with Kong’s axe and destroys the crystal controlling Shimo. Shimo changes sides, freezing Skar King before Kong shatters him to pieces.
After undoing Shimo’s ice age with his atomic breath, Godzilla returns to rest in the Colosseum. Jia decides to stay with Andrews. Mothra restores the protective barrier of the Iwi’s home and the portals. Kong returns with Shimo and Suko to Hollow Earth, where he becomes the ape tribe’s new leader.