The MonsterVerse has revealed that King Ghidorah is the one to blame for Kong having to leave Skull Island in Godzilla vs. Kong. At the beginning of the movie, it was explained that the Titan’s home had sadly become uninhabitable due to a powerful storm that had taken over the island.
At the outset of Godzilla vs. Kong, Dr. Ilene Andrews (Rebecca Hall) and Dr. Nathan Lind (Alexander Skarsgård) had to hurry through the pouring rain to get into Monarch’s Kong containment facility. It was explained that this storm killed Jia’s people, and had become a threat to Kong’s safety as well. Monarch built an additional outpost on the island to protect Kong from the storm, but his size made it hard for them to maintain it. It was because of this storm and the understanding that Kong couldn’t live there forever that Dr. Andrews relented to Dr. Lind and agreed to let him be a part of APEX’s Hollow Earth expedition.
A prequel graphic novel to Godzilla vs. Kong, Kingdom Kong, sheds some light on what the nature of the storm actually is and how it came to be. Dr. Andrews blamed the state of the island on Monarch’s "meddling”, but apparently the situation is more complicated than that. It was said in the story that Skull Island’s storm originated during the events of Godzilla: King of the Monsters. As seen in the film, Ghidorah created massive storms while trying to terraform the planet. Two years after his defeat, one of his storms remained intact over the Pacific Ocean. Dr. Houston Brooks called it a “gift from the devil to remember him by”.
The storm remained there for two years, and suddenly started moving toward Skull Island. Under Brooks’ leadership, Monarch’s forces on Skull Island worked to divert the storm, but their efforts were unsuccessful. Ghidorah’s storm hit the island and caused significant damage because of its ability to create powerful cyclones. A “vortex” in the Hollow Earth entry point under Skull Island resulted in the storm being “anchored” on the island. After seeing how destructive it was and how it hindered Kong’s ability to protect his home, Monarch came to the realization that Skull Island and its inhabitants wouldn’t be able to persevere. As for how Kingdom Kong’s Ghidorah reveal connects to Dr. Andrews’ “meddling” comment, this could be explained by Monarch’s position on the matter. In the graphic novel, Brooks felt that he and Monarch were responsible for not stopping it.
Kong’s home falling to Ghidorah’s storm shows that the damage done by Monster Zero is still being felt, plus it represents just one more consequence of Emma and Jonah’s Titan plan. Because of King Ghidorah, Kong lost the only home he had ever known. Thankfully though, the ending of Godzilla vs. Kong did allow him to transition to a new place in the MonsterVerse by sending him down to the Hollow Earth. His days on Skull Island are over, but now he is free to roam the world of his ancestors.