NOTE: This spoiler was submitted by Jeremy

The film opens somewhere on Skull Island. The great ape Kong awakens and gathers his food on the island before making a spear from a tree. He throws it and it hits the wall of a dome that is using Skull Island as a setting. Kong is being studied by Monarch scientist Dr. Ilene Andrews (Rebecca Hall), and he has developed a bond with a girl named Jia (Kaylee Hottle), a deaf girl from the Iwi tribe whose family was killed by a tidal wave and is now looked after by Ilene. Ilene’s aide thinks Kong should be let go from the facility, but she worries that him being out in the open will lead Godzilla to go after them, as there cannot be two alphas.

It has been five years since Godzilla battled King Ghidorah and established himself as the king of the titans. A new company called Apex Cybernetics, led by Walter Simmons (Demian Bichir) has stepped in to help rebuild society following all the destruction. A former Apex employee, Bernie Hayes (Brian Tyree Henry), runs a podcast, Titan Truth Podcast, discussing his theories on whatever kind of secret work the company is behind. As Bernie tries to gain entrance into the facility, it comes under attack by Godzilla, who lays waste to the place, seemingly unprovoked. After burning half the place down, Bernie notices what looks like a core reactor hidden underground.

Madison Russell (Mille Bobby Brown) sees news of Godzilla’s rampage, leading to everyone thinking he is not as heroic as he once seemed. She goes to tell her dad Mark (Kyle Chandler), who is now working closer with Monarch. Madison doesn’t think Godzilla is naturally destructive, but Mark thinks that Godzilla has given in to these monstrous tendencies. She listens to Bernie’s podcast regularly and overhears him saying how the Pensacola facility is responsible for whatever is going on with Godzilla.

At the Denham University in Philadelphia, Walter visits former Monarch scientist Dr. Nathan Lind (Alexander Skarsgard) with Ren Serizawa (Shun Oguri), son of Ishiro. They approach Nathan over his Hollow Earth theory, as they have detected an energy signal from a potential ecosystem in Hollow Earth. Walter wants the life force from there to fight against Godzilla. Nathan’s brother was lost in a mission traveling toward this location. Walter shows him a vehicle that can get him and a crew down there safely.

Nathan goes to find Ilene, his former colleague, to convince her to use Kong to help locate the Hollow Earth source. She is reluctant to do so, knowing that Godzilla and Kong’s ancestors once fought against each other in a great war and may repeat history, but she gives in. Kong is brought onboard a convoy ship, and the crew is joined by Walter’s daughter Maya (Eiza Gonzalez) to oversee that the operation goes according to plan. While sailing in the pouring rain, Jia goes outside to find Kong roaring in distress. Ilene runs out and learns from Jia that Kong is able to understand and communicate in sign language, and she knows that he doesn’t trust that the crew has his best interests at heart.

Madison gets her friend Josh (Julian Dennison) to go with her to find Bernie. They get a tip from a guy at the nearby convenience store and locate his apartment. Bernie only talks to them when he realizes who Madison’s mother was. He discusses his conspiracy theory with Madison and Josh. She thinks that Apex did something to provoke Godzilla into attacking. Bernie tells them about a large stash of cargo that has made its way to Apex, as well as the tech he noticed earlier.

The crew feeds Kong fish while Ilene asks Jia why she didn’t tell her that Kong can communicate, and Jia says that Kong didn’t want them to know. Not long after, Godzilla makes his way toward the convoy, crashing into them and causing the ship to turn over. Kong is freed from his bonds and goes after the giant lizard. Kong manages to get a couple of good hits in and knock Godzilla back into the ocean, but Big G fires his blue flame toward the sky, causing him to take the advantage and pull Kong underwater with his tail, nearly drowning him. The crew releases depth charges to disorient Godzilla and free Kong, but the ape is wiped out. Ilene tells the convoy’s captain to kill the power to make Godzilla think he’s won so that he can leave. They do so and it works, but they end up getting airlifted to their destination.

Bernie joins Madison and Josh to the rundown Pensacola facility, but when they access the bunker, they find that the core is gone. The three then find an elevator that takes them underground. They come across a chamber containing pods filled with Skull Crawlers, but before they can get out, the chamber is picked up and being transported to Hong Kong.

The crew finds the source of the energy signal in Antarctica. Jia convinces Kong to go through a tunnel where he has picked up the energy source, as it may lead to his home. Kong leads the crew toward the tunnel, which takes them through a portal where gravity is inverted. There, they find Hollow Earth, home to many other titans. Kong encounters winged monsters who attack him and the crew, but he grabs hold of them and smashes one into the dirt. Another tries to strangle and suffocate him, but Nathan’s ship fires at the creature and gives Kong room to tear it apart (and even eat from its skull).

The trio ends up at the Hong Kong Apex facility and discovers what Walter and Ren have really been working on: the “superior” to Godzilla that will put an end to humanity’s titan problem – MECHAGODZILLA. Walter tests its power on an unlucky Skull Crawler, which the trio witnesses. They also discover that Ren is controlling MechaGodzilla using a psionic uplink with one of the skulls of Ghidorah. The trio are then caught and apprehended by Apex guards.

The crew travels deeper into Hollow Earth and comes across the home of Kong’s ancestors. He picks up an axe made from a spike off the back of Godzilla’s ancestors, and he finds his family’s throne room and sits upon it like a true king. The axe activates the energy source in the ground. Maya then sends out Apex spider drones to take out a sample of the source for her father to exploit, despite protests from Nathan and Ilene. From up above, bat creatures descend and attack Kong and the crew, but he fights them off.

On the surface, Godzilla has entered Hong Kong and finds the source leading to Hollow Earth. He breathes down it and sends a blast to charge Kong’s axe. In the chaos, Maya and her team try to shoot Kong down, only for him to grab their craft and crush it in his paw. He then jumps through the portal, with Nathan, Ilene, and Jia following in their craft. Kong takes his axe out and begins Round 2 with Godzilla. They trash the city and demolish skyscrapers, but Kong comes back with a fury by bringing down the axe on Godzilla. His blue flame doesn’t affect it, so Kong manages to bring Godzilla down hard with one swing. However, Godzilla gets himself back up and brings Kong down again with his foot. He roars in Kong’s face, but Kong remains defiant and roars right back at him. Godzilla spares him and starts walking away.

The trio are brought to Walter, who is planning to set MechaGodzilla onto the real Godzilla to establish humanity’s dominance over the creatures. Unfortunately, just as Ren beings the uplink to MechaGodzilla, Ghidorah’s consciousness takes control. MechaGodzilla swings its claw at Walter, killing him, while Ren is electrocuted from the override. The metal beast rises to the surface and goes after Godzilla, beginning to overpower him with its strength and stronger heat blast. When Jia senses Kong’s heartbeat slowing down, Nathan uses the Apex vehicle to deliver a charge powerful enough to revive Kong. When he wakes up, Jia tells Kong that Godzilla is not the enemy. He understands and charges to fight MechaGodzilla before it can deliver the fatal blow to Godzilla. Kong brings his axe down on the giant robot, and Godzilla joins the fight. Realizing Kong is on his side, Godzilla charges Kong’s axe with his fire breath, and the mighty ape starts chopping MechaGodzilla’s limbs off before ripping its head off and showing it off as a trophy.

In the aftermath, Madison reunites with Mark, and he meets Bernie, who wants to have him on the podcast to discuss more Apex and Monarch coverups. Godzilla then rises and looks at Kong, who drops his axe to signify their truce. The titans look at each other as worthy opponents before Godzilla goes back into the ocean.

Nathan and Ilene set up a new research facility in Hollow Earth, which Kong has made his new home. He continues his friendship with Jia and goes about the land, where he is now once again the king.

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Five years after defeating King Ghidorah, Godzilla reappears to attack a facility operated by Apex Cybernetics, a company meant to help humanity rebuild from the titan destruction. Apex CEO Walter Simmons recruits former Monarch scientist Nathan Lind to lead them to an energy source in the fabled Hollow Earth to use against Godzilla. Nathan goes to Ilene Andrews, a Monarch researcher who has been studying Kong for a decade, to convince her to use Kong to guide them to the energy source. Kong has also developed a friendship with a deaf Iwi native girl named Jia, who communicates with Kong via sign language.

On the way to the energy source, Godzilla attacks the convoy and fights Kong for the first time. He nearly drags the great ape underwater until the crew intervenes and scares Godzilla off temporarily, tricking him into thinking he has won. They locate Hollow Earth and find Kong's ancestral home, where his family truly ruled like kings. He even finds an axe made from dorsal spines like those found on Godzilla. Walter's daughter Maya attempts to extract a sample of the energy source just as Godzilla also locates the source and attacks using his fire breath. Kong fights off monsters in Hollow Earth and kills Maya and her crew when they attack him. Kong engages in Round 2 with Godzilla and nearly beats him down with his axe, but Godzilla once again overpowers Kong but spares him.

Meanwhile, Madison Russell gets her friend Josh to find former Apex employee Bernie Hayes, as they know Apex is behind whatever is setting off Godzilla. They come across their facility and find that Apex is using one of Ghidorah's skulls to control MechaGodzilla, which Walter wants to use to assert humanity's dominance over the titans. It backfires when Ghidorah's consciousness takes over, and MechaGodzilla comes to life without the link. It kills Walter and makes its way into Hong Kong where it fights Godzilla and almost kills him. Nathan helps revive Kong, who is convinced to help Godzilla by Jia. Godzilla and Kong team up, using the blue flame/battle axe combo to tear MechaGodzilla to pieces. Godzilla and Kong acknowledge each other as worthy opponents before Godzilla goes back to the ocean.

Kong makes Hollow Earth his new home, with Nathan, Ilene, and Jia still keeping an eye on him.