There's also the possibility that a new, original character could be the main antagonist. This character could be a powerful figure in the society of Remnant who feels threatened by Blake and Jaune's actions or potential, and so uses their influence to have them banished.
Maybe Adam Taurus could be the main antagonist. He has a history with Blake, and he could manipulate events to get Blake banished, and Jaune might be caught in the crossfire. Adam could be seeking revenge on Blake for leaving the White Fang or he might see her as a threat to his own plans.
It could be Cinder Fall. She's always been a major villain in RWBY. She might be the one who arranges for Blake and Jaune to be banished as part of her evil plan to gain more power or cause chaos in the world of Remnant.
One possible plot could be that they are banished due to a false accusation. For example, they might be wrongly blamed for a crime they didn't commit within the RWBY universe. Maybe some powerful figure wants to get rid of them for political reasons.
Perhaps an evil organization that wants to use the power of both Naruto and Blake for their own malicious purposes. They could be from a parallel dimension where they have studied both Naruto's world and RWBY's world. They would try to capture Naruto and Blake, forcing them to fight not only for their own freedom but also to protect the two universes from the organization's evil plans.
Maybe there's a hidden character in the Naruto universe who manipulates Naruto into banishing RWBY. In this case, that hidden character would be the main antagonist. They could be someone with a vendetta against RWBY's world or just wants to cause chaos in both universes.
In some fanfictions, they might team up to prove their worth and get reinstated. They could go on a journey to uncover a conspiracy that led to their expulsion.
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 might be a new character, a powerful being that rules the realm where Percy is banished. This being could see Percy as a threat to his or her power and try to stop Percy from finding a way back.
A powerful sorcerer who also wants to claim the island for his own could be the main antagonist. He sees Percy as an obstacle to his plans and tries to eliminate him. The sorcerer might have control over some of the dangerous creatures on the island and use them to attack Percy.
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.