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.
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.
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.
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.
In such a fanfiction, Naruto might focus on rebuilding the village. He could start new training programs for the young ninjas to ensure the village's future protection.
Another aspect could be Naruto's relationship with the other villages. After Madara, there might be a power shift in the ninja world. As Hokage, Naruto would work towards strengthening the bonds between the villages. He could initiate more joint ninja training programs and diplomatic meetings to ensure long - term peace.
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.
Naruto is obviously still very popular as the main character. His growth and development after the Pein attack are central to many fanfictions. Fans are interested in seeing how he copes and what new powers or skills he might gain.
One possible scenario in a fanfiction where Naruto becomes Pein could be that Naruto is exposed to some dark jutsu that alters his mind. This jutsu might be related to the Rinnegan's power. As a result, he starts to adopt Pein's ideology of bringing pain to the world in order to create peace. His friends would be shocked and try to bring him back to his normal self.