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.
It could be Natsu. He's hot - headed and might not understand Naruto's ways at first. He could see Naruto as a threat to his position in the Fairy Tail guild and start bullying him to assert his dominance.
It could be a dark wizard from the Fairy Tail world who sees Naruto as a threat because of his unique powers. This wizard might try to stop Naruto from leaving, fearing that he'll take the knowledge of Fairy Tail's magic to other places.
Maybe the main antagonist is an outside force that has influenced the Fairy Tail guild to exile Naruto. For example, a dark guild could spread false rumors about Naruto, making the Fairy Tail members believe that he is a danger to them. This way, they can get Naruto out of the picture and then plan an attack on the Fairy Tail guild without having to deal with Naruto's power.
It could be an evil mage from Fairy Tail who sees Naruto as an outsider and a threat to the balance of power in the magic world. This mage might try to use Naruto's neglected past against him, trying to manipulate him into doing bad things.
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.