Perhaps a group of vampires who are trying to take over the entire Rosario Vampire world and are causing harm to both humans and other supernatural beings. Naruto views their actions as unacceptable and makes it his mission to banish them. They could be very strong and have some special abilities that make them a formidable foe for Naruto.
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.
It could be Danzo. He has always been suspicious of Naruto and might see this as an opportunity to get rid of him for good. He could spread false information to make the village turn against Naruto after the Pein attack.
The main antagonist could be one of the village elders. They might see Naruto's fox - summoning abilities as too dangerous and banish him out of fear. Throughout the fanfiction, they could try to prevent Naruto from coming back to the village, fearing that he'll seek revenge or disrupt the power balance they've established.
The main antagonist could be a powerful demon that has been sealed in the Fairy Tail world for a long time. Naruto's arrival disrupts the seal somehow, and the demon sees Naruto as a key to fully breaking free. The Fairy Tail members and Naruto must put aside their differences and combine their powers to fight this demon.