A new, powerful and mysterious ninja from another village could be the main antagonist. This ninja could have abilities that Naruto has never faced before and a very different set of values. He could target Naruto specifically, perhaps seeing him as a threat to his own plans for power or domination. In the struggle against this new enemy, Naruto might be forced to make difficult choices that lead him to a darker path.
It could be Sasuke. If Sasuke continues to pursue his own vendetta in a more extreme way and Naruto's attempts to bring him back fail, Sasuke could become the main antagonist. Their rivalry could turn into a full - blown battle for power and ideology, with Naruto being pushed to his limits and potentially turning dark in the process of trying to stop Sasuke.
It could be an ancient dark wizard who has been manipulating events from the shadows. This wizard might see Elsword as a powerful tool and has been slowly influencing him to turn dark. The wizard could be using dark magic to cloud Elsword's mind and make him more susceptible to negative emotions.
Palpatine could still be the main antagonist even if Luke turns to the dark side. He might try to use Luke as a more powerful weapon against any remaining Jedi or the Rebel Alliance. Palpatine would see Luke's newfound dark side power as a means to further his own control over the galaxy.
Maybe the main antagonist is an ancient spirit that has been awakened by Naruto's experiments with transformation. The spirit doesn't like Naruto's interference with nature's balance and decides to punish him by making him turn into a fox with the strange 'lemon' aspect. This spirit then tries to keep Naruto in this form permanently and drive him mad, so that Naruto can no longer be a threat to the spirit's plans of ruling over the ninja world.
It could be a rogue Dark Jedi who has escaped from his own Order and sees the Naruto world as a new place to spread chaos. He might be seeking powerful chakra sources to fuel his Dark Side powers.
It could be Darth Sidious. He is always looking for powerful allies. If he senses Ahsoka's potential and her growing disillusionment with the Jedi, he might manipulate her into joining the Dark Side. His cunning and power would make him a formidable antagonist in this scenario.
It could be a long - lost moon - dwelling ninja clan that has a grudge against the Leaf Village. They see Naruto as a threat to their plans on the moon's dark side.
It could be Orochimaru. He's always been interested in dark and forbidden jutsu. In this fanfiction, he might have found a way to merge the dark forces of Dark Nights Metal with his own research, becoming an even more powerful and menacing antagonist.
It could be a rogue ninja who is also after the power of the chakra chains. This ninja might see Naruto as a threat and try to eliminate him to get the chains for himself.
It could be an existing villain from the original story who sees Adrien's potential and manipulates him into turning to the dark side. For example, a powerful sorcerer or a mastermind criminal. They could use Adrien's weaknesses, like his desire for power or his need to prove himself, against him.
Perhaps an evil mage who actually intended for the transformation to go wrong on purpose. They might want to use Sans' new female form to cause chaos in the Underground. They could be trying to manipulate Sans into doing bad things or using her to get to other important characters.