There's a possibility that the main antagonist is a rogue ninja from Naruto's own world who has been exiled to the moon's dark side. Over time, this ninja has gained new powers and now wants to use Naruto to get revenge on the ninja world. He might manipulate Naruto's dark side to achieve his own evil goals.
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 a new, powerful dark side user created specifically for the fanfiction. This character might have a vendetta against the Skywalker family and sees turning Leia as a way to get revenge on Luke and Anakin. They could use Leia's insecurities and her desire to protect her loved ones against her.
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.
It could be Hawk Moth. He might finally succeed in corrupting Adrien. Hawk Moth could use Adrien's inner doubts and fears to his advantage. For instance, if Adrien is worried about losing his loved ones, Hawk Moth could promise him a way to keep them safe if he joins the dark side.
It could be the remaining Jedi. Since Luke is turning to the dark side, the Jedi who still uphold the light side values would be against him. They would see him as a threat to the balance they are trying to maintain and would try to stop him from fully embracing the dark side.
Perhaps a powerful dark side cult leader. They could manipulate Ezra into believing that their way is the right one and that the dark side is a misunderstood power. The cult leader might use Ezra's own insecurities and desires to draw him into the dark side.
It could be the remaining Jedi. Since Rey is turning, the Jedi who still uphold the light side would see her as a threat. They would try to stop her from causing more harm with her newfound dark side powers.
It could be an unknown ninja who has been secretly studying dark energon for years. He wants to use it to take over the ninja world, believing that the power of dark energon will make him invincible.
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 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 Dumbledore. In a twisted take on the story, if Harry joins the dark side, Dumbledore would be the one trying to stop him. Dumbledore has always been the guiding force for the good side, and Harry's defection would be a huge blow. Dumbledore would then have to face the difficult decision of either trying to save Harry or stopping him by any means necessary, making him the antagonist from Harry's new 'dark' perspective.