Another possibility is a group of Imperial scientists who are conducting unethical experiments with the Force. They see Luke as a prime specimen and try to control him. They would be the main antagonists as they try to use Luke for their own immoral purposes rather than allowing him to pursue his own agenda within the Empire.
One possible plot could be that Luke is disillusioned with the Rebellion after some major setbacks. Maybe he discovers some secrets about the Rebellion that make him question their motives. So, he decides to join the Empire in the hope of bringing about change from within. He might start off by using his Jedi skills to gain favor among the Imperial ranks.
It could be a Rebel spy within the Empire. This spy would be constantly trying to undermine the OC's progress and expose their true intentions. The spy might see the OC as a threat to the Rebellion's plans, especially if the OC is rising in the ranks quickly.
It could be the headmaster of the imperial academy. They would be in charge of making sure all the students adhere to the Empire's values and teachings. They might see Luke as a potential threat to their regime within the academy and constantly try to undermine him or turn him into a loyal imperial subject.
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 an ancient evil that has been sealed away in the empire for centuries but is released due to the chaos of the crossover. This entity could be more powerful than any foe the Naruto characters have faced before, forcing them to find new ways to fight.
A group of ninja who oppose the new order of the Naruto Empire could be the main antagonists. They might believe that the empire has become too controlling or has strayed from the original values of the ninja world. They could use guerrilla tactics and create internal unrest within the empire to try and bring it down.
It could be the remaining Jedi. Since Luke has joined the dark side, the Jedi who still uphold the light side would be his natural antagonists. They would see him as a threat to all they stand for and would try to stop him from spreading the influence of the dark side. For example, Leia, if she still adheres to the Jedi teachings, would be in direct opposition to Luke.
If Luke joined the Empire in a fanfic, it would be a complete deviation from his original path. He might use his Force abilities to rise quickly within the Empire's ranks. However, his friends like Han and Leia would likely become his enemies, leading to intense and tragic confrontations.
Maybe the old Imperial warlords who are against any kind of reform. They are used to the old ways of the Empire and don't want Luke and Mara to change things.
It could be a senior officer who has a grudge against Percy for some reason. Maybe Percy accidentally made him look bad in front of the higher - ups early on.