Perhaps it could be a minor character from the original Naruto series who was banished for some reason. They then transform into an assassin and their story of revenge or redemption becomes the central plot. For example, someone who was always on the fringes in the village and had a grudge that led to their banishment and new path as an assassin.
It could be an original character. For instance, a ninja who was wrongly framed for a crime and banished. They would then be the focus as they navigate their new life as an assassin.
Another option could be Kakashi. Suppose he is banished because of some incident related to his Sharingan. He has so much history and experience, and seeing him outside of the village structure, relying only on his Sharingan and his wits, would make for a great story. He could also have flashbacks to his past experiences with the Sharingan while dealing with the challenges of being banished.
It could be an original character created by the fanfic author. This character might be a skilled fighter, maybe with a unique weapon or fighting style, like using a special kind of kunai combined with lightning - based chakra attacks.
It could be an original character. For example, a ninja who was born into a minor clan but had great potential. However, due to political intrigue and jealousy from a major clan, he was framed and banished. He then became a mercenary to survive. Another option could be a character who was once a part of a secret ninja organization and was banished when he disagreed with their methods. Now, as a mercenary, he returns to the Naruto world with a vendetta against those who wronged him.
It could be Danzo. He has always been a shadowy figure with his own agenda. He might see Naruto as a threat to his control over the village and engineer his banishment.
It could be a powerful Thalmor agent. The Thalmor are often seen as the bad guys in Skyrim, and if Naruto shows up, they might see him as a threat to their plans of domination. They could use their influence to get Naruto banished and then try to hunt him down.
The main antagonist could be a powerful Sith - like figure who has infiltrated the ninja world. This character might be manipulating events from the shadows, causing the village to suspect Naruto and leading to his banishment. They could have their own motives for wanting to take over the ninja world, like using its chakra for their own dark purposes.
Maybe the main antagonist is a group within Naruto's own village. The elders or some of the more conservative clans who banished Naruto in the first place. They fear that if Naruto returns as the banished emperor, he will change the power structure that they have been maintaining for so long. So they do everything they can to stop him from coming back, even if it means allying with outside forces.
A powerful Hollow could be the main antagonist. This Hollow could sense Naruto's unique energy and see him as a threat to its plans of taking over Karakura. It might constantly target Naruto and his new friends, trying to eliminate them one by one.
The main antagonist could be a power - hungry elder in Temari's own village. This elder might see Temari as a threat to their authority, especially if she has been getting too much influence or support from other ninja. So, they frame her for a crime that leads to her banishment.
It could be a rogue ninja from a neighboring village who wants to obtain Naruto's Rinnegan for himself. This ninja has been secretly observing Naruto and sees the potential of the Rinnegan. He then tries to hunt Naruto down during his banishment to take the power.