Three years after defeating Mechagodzilla, Kong has established his new territory in Hollow Earth and searches for more of his kind. On the Earth's surface, Godzilla continues to maintain order between humanity and giant monsters, known as "Titans"; killing Titanus Scylla for attacking Rome, Italy, and resting in the Colosseum.

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 in school, causing her adoptive mother, Kong expert Dr. Ilene Andrews, to worry. 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.