Kong’s species may have been the villains of the first Titan War discussed in Godzilla vs. Kong. Although there’s no question that Kong himself is a hero in the MonsterVerse, it shouldn’t be taken for granted that the same was true for his ancestors. It’s possible that Godzilla and Kong’s roles were flipped in the original Titan War.
Godzilla vs. Kong confirmed the teases from Kong: Skull Island and Godzilla: King of the Monsters that pointed toward the two rival alphas having a violent history that goes back thousands of years. Rebecca Hall’s character, Dr. Ilene Andrews, mentioned a legend passed down by the Iwi tribe that described an ancient conflict between Godzilla and Kong. Apparently, other members of their species battled it out over several millennia ago in the Hollow Earth, with one of their fights taking place in Kong’s temple. The movie didn't reveal who won, but the implication was that things didn’t work out well for Kong’s kind, considering they deserted their home and relocated to Skull Island. This detail indicated that Godzilla’s species must’ve driven them out.
If it’s true that Godzilla forced the Kongs out of the Hollow Earth, that means he may be indirectly responsible for the near-extinction of their species at the hands of the Skullcrawlers. But even if that is the case, it could be that it was Kong’s ancestors – and not Godzilla’s – that were the Titan War’s real villains. In the Godzilla vs. Kong novelization, it was noted that the Iwi interpretation of how the first Titan War started is that the Kongs thought Godzilla was “evil” and banded together in an effort to make him leave the Hollow Earth. But while they believed Godzilla to be an “evil” creature, it was never stated that he actually did anything wrong. Instead, it was heavily implied that Kong’s ancestors struck first blood.
One of the biggest clues that support the conclusion that they were the villains is the Mothra Easter egg in Godzilla vs. Kong’s opening credits. For a reason that hasn’t been explained, Mothra was included in an old painting of the Titan War. Presumably, she was fighting alongside Godzilla against Kong. When figuring out Mothra’s role, it’s important to understand both her connection to Godzilla and her place in nature. Mothra is a benevolent guardian monster and a symbol of purity. The MonsterVerse’s Godzilla is a hero too, but it’s much easier to see him as a villain than it is Mothra, who is always depicted as a force for good. Plus, she’s not the type to care about Titan rivalries. That’s why she must have been justified if she was helping Godzilla beat the apes. As for the chances of Mothra siding with Kong instead, it’s unlikely that she and Godzilla would have the symbiotic relationship that they share in King of the Monsters if that had happened.
In short, Mothra being in the Titan War and the Kongs’ preemptive attack on Godzilla in the Iwi legend provide evidence for Kong’s side being the instigators of their original fight. This would draw an interesting parallel to Godzilla vs. Kong, where it was clearly Godzilla who was the perpetrator. It also adds a bit more depth to their history and Godzilla’s motivations for tangling with Kong. It could be that he recognized the ape as a member of the same species that wrongly tried to force his kind out of the Hollow Earth all those years ago.