Five years after Godzilla killed his extraterrestrial nemesis Ghidorah, he and Kong are currently the last known active Titans on the Earth’s surface. On Skull Island, the climate has been destabilized. Monarch now watches over Kong, who resides within a giant dome. Kong is visited by Jia, the last Iwi native and Ilene Andrews’ adopted daughter, who is deaf and can communicate with Kong via sign language.
Bernie Hayes, a former employee of the Apex Cybernetics corporation and host of a Titan conspiracy theory podcast, exfiltrates information suggesting sinister activities at a Pensacola Apex facility. However, Godzilla suddenly attacks the facility; during the rampage, Bernie discovers a device that resembles the ORCA, previously used to communicate with or control Titans. Madison Russell, a fan of Bernie’s podcast, enlists her friend Josh to investigate the cause of Godzilla’s attack.
Together they find Bernie and sneak into the wrecked Apex base, discovering a secret facility deep underground. They are inadvertently locked and transported in a container carrying Skullcrawler eggs (two-legged reptilian megafauna that was previously discovered by Monarch) through an underground tunnel to Hong Kong.
There, they unwittingly intrude on a test of Mechagodzilla, a mechanical version of Godzilla, telepathically controlled by Ren Serizawa, the son of the late Ishirō Serizawa, through the neural networks of Ghidorah derived from a severed head that Apex had managed to retrieve. The test is cut short due to limitations of the power supply. It is then revealed that Walter Simmons (Apex executive) intends to harness to power of an energy source in the Hollow Earth, an underground world that is below the Earth and the secret home to the Titans, to overcome the limitations of Mechagodzilla.