Maybe a group of bounty hunters hired by the remaining Imperial forces. They see Luke as a big threat and Captain Rex as an annoyance. They keep hunting them down throughout the story, creating all sorts of dangerous situations for our heroes.
Another possibility is a dark side cultist. They sense the power in Luke and want to either turn him to the dark side or eliminate him. And they view Captain Rex as an obstacle in their way of getting to Luke, so they target both of them.
One possible plot could be that Luke is on a mission in a far - flung part of the galaxy. There, he stumbles upon Captain Rex, who has been in hiding for years. Rex recognizes Luke as Anakin's son and decides to share his experiences of the Clone Wars with Luke, teaching him valuable lessons about war, loyalty and the Jedi.
An alien race with a grudge against the Republic could also be the main antagonist. They might target Rex specifically because of his strategic importance and his role in leading many successful missions against them in the past. His death at their hands would be a major blow to the Republic's morale.
A good antagonist could be a rogue S.H.I.E.L.D. agent who has his own plans for power. He might see Captasha and Black Widow as threats to his scheme. This agent could have access to some high - tech weapons and a group of loyal but misled followers.
It could be a powerful alien warlord who has set his sights on Earth. This antagonist might have an army of powerful minions and technology that rivals Captain Marvel's and the Avengers' combined powers.
It could be a rogue Amazon who disagrees with the idea of an outsider like Captain America being on Themyscira. She might see him as a threat to their way of life and try to drive him out, or even worse, harm him.
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.
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 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.
It could be a powerful warlock who has found a way to manipulate time and space. He wants to stop Paige and Prue from joining forces because he fears their combined power. So he creates various obstacles and illusions to keep them apart.
Maybe a powerful rogue ninja who has discovered a way to steal the powers of divine entities. He sets his sights on Amaterasu and Naruto because he knows that if he can combine their powers, he will be unstoppable. He creates various traps and illusions to separate them and weaken them so that he can carry out his evil plan.