Asking why Kong had to leave Skull Island might bring up a few different answers, but the comic book version of Kong could possibly offer one explanation that people might like. For one, we already knew that a tropical storm had decimated Skull Island and killed the natives, and might have killed Kong if not for Monarch’s ability to step in and create a habitat for the big ape that kept him secure from the tempest. But it’s revealed that the storm is a parting gift from King Ghidorah and thanks to a vortex that is present on the island thanks to a passage that leads to the hollow earth, the storm continues unabated. Plus, the fact that Ghidorah’s consciousness is somehow still bound up in the skull that’s being used to power up Mechagodzilla has something to do with it, so Kong couldn’t stay put for long for a few reasons, one of the most obvious being that Godzilla would have found him eventually. But it was obvious that Kong wasn’t happy with his enclosure since launching a tree at the panels showing a clear sky was a good sign that he was ready to get out. But where one puts a giant ape is a good question, especially in a world where the titans have already ravaged so much and left behind a wake of destruction that has some humans desperate enough to create their own kaiju killer, which in retrospect was a very bad idea.
One question that’s harder to answer is why Godzilla was attacking Kong in the first place. There’s more than one theory about this since the simplest thing to say is that they’re rivals, and always have been, and rivals fight, so there’s one easy explanation. But apart from that, Kong was happy enough in his place on Skull Island, and obviously ignored the call that went out from Ghidorah. Some like to think that Godzilla felt slighted that Kong didn’t bow to him as the other titans did, but that feels a little thin when it comes to serving as an explanation. The rivalry explanation makes a lot more sense, and the idea of Godzilla drawing Kong out, which still wouldn’t have worked since Kong didn’t really care about much except his island and the people he protected. If anything, this makes Godzilla look like a vain jerk and Kong the chill protector that doesn’t want much apart from his place in the world. But once he was taken from his home and shown the hollow earth region it became kind of obvious that he felt right at home, as genetic memory was able to guide him to the throne room where his ancestors had obviously tangled with Godzilla’s kind in the past, judging by the ax that had been created and the skeleton that was found on the floor. Godzilla was definitely made into more of a villain for a while in this movie since he had no trouble blasting about randomly as he sought out the project that was putting out the signal he didn’t like in the Apex labs. To be fair, Apex was doing something incredibly dangerous, and Godzilla was trying to stop it, but at most times it felt more like petulance than safeguarding the world.
If anything, it felt as though Godzilla was exerting his influence in a big way, especially when it came to attacking Kong while he was still in transit to the hollow earth site. His need to be THE only titan left was kind of an obsession that was almost the end of him since Mechagodzilla was wiping the streets with his scaly hide while Kong lay dying from their previous encounter. I’ll keep saying it, Kong never knelt to Godzilla, and it’s likely that he never will since the two titans had to come to grips with the reality that neither of them would back down, and Godzilla did win. It’s a hope that there won’t be a sequel, but if there is then it would be nice, if the titans do get into a scrap again, to see Kong remember Godzilla’s tactics and find out whether or not he can counter the big lizard this time around. Plus, if Kong does keep growing it’s likely that he could overpower Godzilla at one point. It was a good fight, there’s no doubt of that, but Godzilla possesses too many natural weapons, and while Kong can definitely swat Godzilla around a bit he’s a little outmatched. But if there is another movie it feels likely that Kong would be likely to recall a few things about the first battle and might be able to use his environment to better effect. If nothing else, it’s fair to say the two titans parted ways with an understanding that they each had a purpose in the world, and that destroying each other was no longer a priority.