Three years after triumphing over Mechagodzilla, Kong finds himself firmly established in the Hollow Earth, seeking to uncover more of his kind. Meanwhile, on the surface, Godzilla vigilantly regulates the balance between humanity and the colossal beings known as Titans. A prime showcase of this includes Godzilla’s decisive defeat of Scylla in Rome, followed by a restful period in the historic Colosseum.
The organization known as Monarch believes that peace can be upheld as long as Kong and Godzilla maintain their territorial boundaries. Kong occasionally emerges from his subterranean lair when he requires medical assistance, such as on an occasion where his tooth becomes infected. Here, Trapper (played by Dan Stevens) steps in to aid him. As Kong attends to his needs, Monarch remains cautious, recalling how close Kong came to losing his life during their last encounter and hoping to prevent a recurrence of such chaos.
However, a Monarch observation outpost stationed in the Hollow Earth detects an unidentified signal. On the surface, this signal triggers hallucinations and unsettling visions in Jia (Kaylee Hottle), the last living descendant of the Iwi tribe from Skull Island, sparking concern in her adoptive mother, Dr. Ilene Andrews (Rebecca Hall). With a sense of urgency, Andrews enlists the help of podcaster Bernie Hayes (Brian Tyree Henry) to analyze the peculiar signal. After extensive exploration, Bernie deduces that the signal correlates with significant titan events from the past, suggesting it is a distress signal directed towards Godzilla.
Having sensed the call, Godzilla departs from Rome to strike a nuclear facility in France, seeking to absorb its radiation, before heading to the lair of Tiamat in the Arctic—a tremendous energy source. In a fierce battle, Godzilla tears Tiamat apart and claims its energy reserves, leading Monarch to speculate that Godzilla is gearing up for a potential threat.
Simultaneously, Kong discovers a hidden realm after a sinkhole opens near his territory and encounters a tribe of his species, including a young ape named Suko. Initially at odds, Kong eventually persuades Suko to guide him to the tribe's shelter; their bond deepens as they face various obstacles together. Suko’s attempts to test Kong’s strength by pitting him against formidable creatures only instill confidence in the young ape regarding Kong's prowess.
However, their respite is short-lived. The tribe's oppressive ruler, the Skar King, seeks to dominate Kong with the help of an ancient ice-powered Titan named Shimo, who he controls with a painful crystal. In their intense battle, Shimo’s icy breath inflicts severe frostbite on Kong’s arm, but with Suko’s support, Kong makes a harrowing escape, albeit without his prized axe.
Meanwhile, Andrews, Jia, and their companions—Titan veterinarian Trapper and conspiracy podcaster Bernie—journey into the Hollow Earth to uncover the signal's origin, arriving at a devastated Monarch outpost. Pressing forward, they stumble upon a hidden temple behind an organic bio-luminescent barrier, leading them to a surviving Iwi community that communicates telepathically. Here, they deduce that the signal served as a distress call from the Iwi.
As Jia engages with the Iwi, Andrews confides her anxiety to Trapper, fearing that Jia may choose to remain with her people, which would leave Andrews alone once more. Inside the temple, they discover hieroglyphics depicting a tumultuous history: the Skar King once attempted to seize the surface world, igniting conflict with Godzilla's lineage, only to be vanquished and sealed deep within the Hollow Earth. With knowledge of Kong's entrance, the Iwi had initiated distress signals to summon aid from Godzilla and Jia.
Furthermore, a prophecy suggests that Jia holds the key to reawakening Mothra, the guardian of the jump points between Hollow Earth and the surface. In a remarkable moment, Kong, drawn by the presence of Jia, finds the temple where Trapper has crafted a prototype exoskeleton arm brace to counteract the frostbite. The brace had been readily available at Outpost One.
Unbeknownst to them, a loyalist of the Skar King has trailed them. This antagonist informs the Skar King, who begins assembling a formidable invasion force against Earth. Miraculously, Jia manages to revive Mothra, enhancing their chances of survival.
Godzilla, having absorbed cosmic energy in Tiamat's lair, undergoes a transformation, resulting in an evolution marked by magenta dorsal plates. In a strategic move to garner Godzilla's support, Kong surfaces in Cairo and attempts to reach out to him. However, their connection falters as a furious Godzilla assaults Kong, initiating a brief but intense confrontation until Mothra, accompanied by Jia, persuades Godzilla to aid Kong's cause.
United, the trio descends into the Hollow Earth to confront the Skar King and the menacing Shimo. Their clash escalates to Rio de Janeiro, where Shimo is commanded to unleash another ice age, unleashing torrents of freezing air that obliterate the sun. As the confrontation intensifies, both forces struggle for dominance, ultimately resulting in widespread devastation across the city.
The decisive moment arrives when Suko returns, wielding Kong's axe and destroying the crystal that enslaved Shimo. Freed from torment, Shimo heeds Godzilla’s guidance and turns against the Skar King. In an epic finale, Shimo and Kong freeze and shatter the Skar King’s reign.
After vanquishing Shimo’s devastating ice age with his atomic breath, Godzilla finds rest once more in the Colosseum. In a heartfelt reunion, Jia reassures Andrews by choosing to remain with her adoptive mother, while Mothra reinstitutes the protective barrier around the Iwi's community before departing. In a new chapter, Kong embraces his role as the leader of the ape tribe alongside Shimo and Suko, returning to the Hollow Earth, setting a course for a promising new era.
