Maybe an entire group of Dark Jedi who view the ninja as inferior beings and want to subjugate them. Their leader, a powerful and cunning Dark Jedi, could be the main antagonist. He would be the one devising plans to take over the Naruto world, using his knowledge of the Dark Side and the Force to outwit the ninja.
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.
The Jedi Council themselves could be the main antagonists. Since they are the ones betraying Naruto, they would be the ones he has to oppose. Their actions of betrayal would drive the conflict in the story.
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 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 the leader of the dark guild. This person would likely have a very different ideology from Naruto's. Maybe the leader believes in using extreme and unethical means to gain power, like sacrificing innocent lives for dark magic. Naruto would constantly clash with this leader as he tries to uphold his own values.
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.
The Jedi Council could be the main antagonists. They are the ones with the power to excommunicate Naruto. Their strict adherence to the Jedi Code and their inability to understand Naruto's different perspective would put them at odds with him.
Perhaps an old member of a forgotten clan who was exiled because of his dark blood. He returns with a vendetta against the village that shunned him. He sees Naruto as a symbol of everything he hates and tries to destroy him. The main antagonist could also manipulate other ninja to turn against Naruto by spreading fear about his dark blood.
Perhaps a group of dark side cultists could be the main antagonists. They idolize the power of the dark side and see Ahsoka as a prime candidate to join their ranks. When she refuses at first, they start to hunt her down, but in the process, they unknowingly push her closer to the dark side, creating a complex dynamic where they are both the pursuers and the inadvertent cause of her fall to the dark side.