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.
Maybe Naruto's connection to Pein through the Nine - Tails is misinterpreted. Since Pein was after the Nine - Tails, the village believes Naruto is a liability. Banished, Naruto wanders into a hidden land where he learns ancient ninja techniques that are far more powerful than what he knew. He could then return to the village as a changed and more powerful ninja, but with a sense of bitterness towards those who banished him.
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.
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.
Naruto might start to question his own identity. Being banished makes him feel like he doesn't belong anywhere. He could then start to explore his Namikaze heritage more deeply. He might discover secrets about his father that were hidden from him, and this knowledge could give him new strength and purpose. He could also use this newfound understanding to try and redeem himself in the eyes of the Hidden Leaf.
In the 'Naruto Hokage after Pein' fanfiction, Naruto may face challenges in uniting the different clans. After the destruction caused by Pain, there would be a lot of mistrust and internal conflicts. He would have to use his new - found respect as a hero to bring everyone together and work towards a better future for Konoha. He might also start training a new generation of shinobi with a different philosophy, one that focuses more on peace and cooperation rather than just power.
Obviously, Naruto is one of the main characters as the title implies he's the Hokage after Pein. Sakura could also be a main character as she is one of Naruto's closest friends and a strong ninja in her own right. Kakashi might also play an important role, as he has always been Naruto's mentor in a way.
Naruto might also initially feel a sense of abandonment. However, his kind - hearted nature could lead him to try and see the good in the situation. He could start to explore the world outside, learning about different cultures and ninja techniques. He may use this experience to become more empathetic towards others who have also faced hardships, and in the long run, this banishment could be a turning point in his life to become an even greater ninja.
One interesting plotline could be Naruto's struggle with PTSD after the Pein attack. He might have nightmares and flashbacks during his training or even in the middle of conversations, which could add a new layer of depth to his character.