Kong and Jia's relationship is genuinely touching. His surprising gentleness toward what is essentially an ant to him is particularly heartwarming. And his ability to communicate with her via sign language is a beautiful demonstration of Kong being an intelligent creature with the capacity to care for others.
Before he destroys the H.E.A.V with Maia in it Kong briefly peeks inside to make sure that Jia isn't inside before destroying it.
After barely surviving Godzilla’s assault on them at the Tasman Sea Jia makes sure to let the tired but still alert Kong “thank you” for protecting them. Kong on his part seems finally able to let himself relax upon seeing that she is safe.
Madison is not so quick to pass judgement on Godzilla and insists that something must have provoked him, possibly after seeing his capacity for benevolence in the previous film. Several others, including her father, agree with her.
Remember Mark went from advocating for the destruction of all Titans especially Godzilla in the last movie, due to blaming the latter for the death of his son, to realizing Godzilla wasn't their enemy and the Titans were needed to protect Earth from worse threats.
Nathan saving Kong's life twice in the film. It's shown several times that he's nervous and downright fearful to get too close to Kong. But that never stops Nathan from putting his own life on the line to save Kong in moments that would have left him dead for sure. First when Godzilla flips the ship Kong is chained and nearly drowns on, Nathan dives into the submerged command center to free Kong while nearly drowning himself. The second is using the HEAV to jump start Kong's heart after his beatdown from Godzilla. And at the end, he's part of the team monitoring Kong in the Hollow Earth, speaking with casual confidence as Kong goes for his "morning walk."
Having fought tooth and nail and even having Kong at his mercy, Godzilla spares him and walks off. Remember, Godzilla and Kong's species were Alpha rivals and had been at war for a long time and it's implied Godzilla had actually been part of that war. So, Godzilla sparing Kong shows the true depth of his compassion and proves how wrong the people in the film who denounce the Titan as nothing more than a monster actually are.
It also hints at Godzilla's lack of malice: He only kills other Titans if he absolutely needs to. The Mutos were threatening to breed and were specifically seeking him as a radiation source, on top of being parasites that had killed off the rest of his species, and Ghidorah was an extraterrestrial threat actively plotting to destroy the Earth. Kong, however, is no threat to the planet and at worst is just an annoying challenger, interfering with his mission to find Ghidorah's signal. Godzilla doesn't find it necessary to kill him, just remind him who's boss and order him to stand down.
Nathan comforting crying Jia by saying she is a brave little girl. Although he accidentally calls her a coward after she called him one by Hiding Behind the Language Barrier early in the film. She smiles however and understands what he was trying to say. She points back to imply she thinks he brave too.
Mechagodzilla has Godzilla dead to rights and is preparing to kill him while Godzilla can only helplessly watch in the first time we ever see the King of the Monsters himself genuinely afraid for his life. Then in comes Kong, pummeling Mechagodzilla to save Godzilla's life, and the look of surprise and relief on Godzilla's face is truly a sight to behold. Godzilla returns the favor when Mecha G sets his sights on Kong.
Adding to this from Kong’s perspective, he had every right to be angry about nearly dying from Godzilla’s brutal beating that nearly resulted in a fatal heart attack for Kong. Kong saving Godzilla’s life after being convinced Godzilla was not the true enemy and that Mecha-Godzilla was truly the one instigating the conflict shows that Kong is capable of showing compassion even to enemies, which ends their battle for good and results in a peaceful end of the battle between the two Titans.
After Kong starts moving again, Jia tells him Godzilla isn't his enemy, something that Kong roars in anger over. She points to Mechagodzilla as the real enemy. While Kong is enraged at Godzilla, because Jia says Mechagodzilla is the true enemy, Kong intervenes to save Godzilla. For the sake of someone he considers family, Kong will put aside even a grudge with the one who nearly killed him.
Even as Jia signs to Kong about getting back into the fight, she tells him "Please. Be Careful." She knows she is sending him into harm's way and wants him to know she cares. It's that message that makes Kong understand what he's fighting for.
Godzilla and Kong gaining mutual respect for one another. Godzilla is still by far the definite winner: but he acknowledges Kong as a Worthy Opponent and departs in peace, Kong becoming the king of the Hollow Earth while Godzilla retreats to the sea with a notable smile on his face.
For his own, Kong initially appears willing to continue the fight, but when he and Godzilla make eye contact, and he considers what they just went through, he drops the axe, signifying the end to the feud between their two kinds.
Kong's actually sitting down and taking a breather after killing Mechagodzilla, when he hears Godzilla's roar and scrambles to his feet, ready to defend himself. But he sees the Big G standing a ways away and looking at him, ready to defend himself but not aggressive. Kong gets the message: there's no need to continue this. For his part, Godzilla's roar seems to be a simple "Hey, Kong!" with his look afterwards saying "Well done. Thanks."
The ending, with Kong making Hollow Earth his new home. After almost 80 years of his story having a tragic outcome, Kong finally gets a real happy ending.
Humans taking Kong off Skull Island has never ended well, with him rampaging and being put down because he just doesn't belong outside his native habitat. Now? Skull Island has been devastated by the perpetual storm and it can't support him any longer. Kong is taken from the Island not to exploit him, but to relocate him to a place where he can live safe and free.
Jia told Kong that his family might be in the Hollow Earth. It turns out she was right... Jia and her adopted mother move to the Hollow Earth, staying with him and greeting him each day he gets up, just like they did on Skull Island.
Pay attention to how Monarch is keeping tabs on Kong from the beginning of the film to the end. Before moving him, they kept Kong in a containment outpost on Skull Island. Now as they set up shop in the Hollow Earth, they're not doing anything to contain him. In fact, their purpose in the Hollow Earth is to act as a monitoring station to watch Kong in his new home.
Also worth noting is that Kong's actually smiling when he signs the word "Home" to Jia. Spending most of the film in captivity, either via containment or in chains, on top of never having a happy ending in all of Kong's cinema history, it's extremely heartwarming that Kong is finally free to roam in his new home, and for the first time, actually feel happy.
