Perhaps a new character could be introduced. Someone who is interested in Naruto's godlike powers for their own evil purposes. This new antagonist could be chasing Naruto during his banishment, trying to either steal his powers or use him for some dark plan.
It could be the village elders. Since they banish Naruto, they could continue to be the main obstacle in his path. They might try to prevent him from coming back or try to eliminate him if they think he's a threat to their power and the village's stability.
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.
One possibility is that Naruto's new 'godlike' powers after the Pain arc are seen as a threat by the village elders. They fear he might become uncontrollable, so they banish him. This could lead to Naruto exploring new lands, meeting new allies or enemies, and potentially finding a way to prove his worth and return.
Perhaps a secret organization within the Hidden Leaf that wants to take over the village. They use Naruto as a scapegoat, getting him banished so they can carry out their evil plans without interference from Naruto. They would be the main antagonists as they are the ones behind the false accusations and the push for his banishment.
One possible plot could be that Naruto is wrongly accused of something after the Pein attack. Maybe the village leaders believe false rumors that Naruto was in cahoots with Pein somehow. As a result, he is banished. He then goes on a journey to prove his innocence and in the process, he discovers new powers and allies. He might also encounter some of Pein's former followers who have their own motives and secrets related to what really happened during the attack.
It could be some of the village elders. They were the ones who decided to banish Naruto, so they could continue to oppose him even when he's in exile. They might see his growing power and influence as a threat to their traditional ways of running the village.
It could be some of the traditionalist elders in the Hidden Leaf. They might see Naruto as a threat even after the war, fearing his growing power and influence, and thus engineer his banishment. So they could act as antagonists as Naruto tries to find his place outside the village.
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.