A few years after the defeat of King Ghidorah, a devastating storm system has taken over Skull Island, wiping out most of the natives and creatures there except for Kong, who is being contained in a biodome, and a deaf girl named Jia. As Kong begins to outgrow his restraints, the facility’s leader, and Jia’s adoptive parent Dr. Ilene Andrews worries that attempting to move him may provoke Godzilla into attacking them, due to the two species sharing an ancient rivalry.
Meanwhile, conspiracy theorist and podcaster Bernie Hayes infiltrates the secretive company Apex Cybernetics, where he uncovers secret plans for a mass shipment to Hong Kong, as well as a mysterious device being held within the facility. Before he can investigate further, Godzilla emerges from the sea and trashes the facility, one of several attacks which has led many to believe that Godzilla has turned on Humanity. Madison Russell doesn't believe so, and after hearing Hayes’ podcast about how something is provoking Godzilla, she sets out with her friend Josh to find him.
Monarch Geologist Nathan Lind is approached by the head of Apex, Walter Simmons, who wants to start an expedition into the fabled Hollow Earth in search of a power source that could help create a weapon capable of stopping Godzilla. Although Lind is skeptical of such a possibility, Simmons shows off a powerful vehicle known as the H.E.A.V (Hollow Earth Anti-gravity Vehicle) that might be able to help humans survive the journey. Needing a guide, they formulate a plan to have Kong lead them down through a passage in Antarctica. Andrews is also convinced, as she hopes to relocate Kong there for his safety.
Madison and Josh team up with Hayes, and they break into the old Apex facility, discovering a massive underground base, where multiple cargo containers are being shipped out. Getting trapped in one, they find it to be full of Skullcrawler Eggs, which are being shipped to Hong kong.
As Kong is being transported, Lind, Andrews, and Jia are joined by Maya Simmons, along with others loyal to Apex. When Kong starts to grow restless, Jia goes out to meet with him and surprise the crew by showing that she can communicate with him via sign language. Suddenly, Godzilla appears and destroys the surrounding fleet. Kong is freed, and the two engage in a brief scuffle before Godzilla gains the upper hand and drags him underwater. They are separated using depth charges, and Godzilla swims away. With the ships destroyed, Kong is brought the rest of the way by air.
Madison’s group arrives at the Apex facility in Hong Kong and sees Simmons unleash a humongous Mechanical creature known as Mechagodzilla, who in a test run kills a colossal Skullcrawler with ease. Mechagodzilla is piloted by Ren Serizawa, son of the late Ishiro Serizawa who resents his father and hates Godzilla and the Titans. Continuing through the base, they find that the robotic titan is being partially controlled by the brain of King Ghidorah, realizing that this is what must be provoking Godzilla, shortly before being caught by Apex security.
Kong leads the group into the Hollow Earth and heads into what appears to be a massive temple. There, he finds the corpses of other dead titans, along with an axe made of one of Godzilla’s spines, which he can charge using some crystals lying around the temple. Maya collects one of the crystals, and sends it to Simmons, before turning on the Monarch agents.
Above ground, Godzilla arrives in Hong Kong and moves towards the Apex facility. Suddenly stopping, he uses his atomic breath to drill through the ground into Kong’s Hollow Earth temple. Kong kills Maya and the other Apex soldiers when they try to escape, before rushing to the surface, along with the other humans. There, he faces off against Godzilla and can counter his Atomic Breath with his Axe, but Godzilla still maintains the upper hand, brutally beating him, and leaving him to die.
Madison’s group is brought up to Simmons, who is preparing to use the crystals to fully power up Mechagodzilla. It initially works, but the power suddenly overloads the systems, allowing Ghidorah to take control. Smashing Simmons and fatally electrocuting Ren, he starts rampaging throughout the city, closing in on an exhausted Godzilla, and beating him to within an inch of his life. While this is happening, Andrews and Lind come up with a plan to revive Kong by overloading one of the H.E.A.V’s reactors. It works, and Jia is able to convince Kong to help Godzilla.
Kong comes in the nick of time, and together the two are able to defeat the artificial Titan, with the help of some last-minute sabotage by Hayes and Josh. After the battle, Kong initially believes he has to fight Godzilla again but ultimately drops his axe to show he's no threat, allowing both to part on peaceful terms. Kong then takes up permanent residence on the Hollow Earth, with Nathan, Jia and Andrews accompanying him while helping Monarch keep track of his activities.
