It could be a corrupt Jedi within the Order. This Jedi might see Naruto as a threat to his own power or status. He could manipulate the situation and convince the other Jedi that Naruto is a danger, leading to Naruto's excommunication. So, this corrupt Jedi would be the main source of conflict for Naruto throughout the fanfic.
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.
Well, in such a fanfic, Naruto's exuberant personality could be the root cause. The Jedi Order is known for its discipline and control. Naruto, with his loud and often impulsive nature, may break too many rules. For example, he might use his chakra in ways that the Jedi consider dangerous or unethical. His refusal to conform to their teachings about suppressing emotions could also play a part. So, they excommunicate him, and he has to find his place in a universe that is not his own.
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.
One idea could be a crossover where a Naruto character, like Naruto himself, somehow gets transported to the Star Wars universe of Jedi: Fallen Order. He could learn the ways of the Force while also using his ninja skills. For example, his shadow clone jutsu might be mistaken for a Force ability at first.
A powerful rogue ninja who has discovered a way to control digital creatures could be the main antagonist. This ninja might see Impmon as a key to unlocking even greater power and would stop at nothing to capture him. He could use his knowledge of ninjutsu and his new - found ability to manipulate digital entities to create chaos in both the ninja world and potentially the digital world if he were to gain access to it through Impmon.
It could be a rogue ninja who has mastered parkour to an extreme level. He uses his skills to steal important ninja artifacts and Naruto has to stop him. This antagonist would be very fast and agile, making it difficult for Naruto to catch him using normal ninja techniques.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.
It could be someone from Miku's world who follows her into the Naruto universe and has evil intentions. Maybe a jealous rival who wants to stop Miku from becoming popular in the new world.
It could be a rogue ninja who wants to use the mummy's power for evil. He might have discovered some ancient scrolls that told him about the mummy's potential and is now trying to awaken it fully and control it to take over the ninja world.
It could be Orochimaru. He has always been interested in the power of the dead and bringing back the strong. He might have found a way to reanimate Naruto for his own evil purposes, like using Naruto's power to take over the ninja world.