Perhaps Naruto, as Hokage after the war, would strive to improve relations with other villages. He might initiate diplomatic meetings and cultural exchanges. For example, he could send Konoha's ninjas to teach in other villages and vice versa, which would strengthen the bonds between them and prevent future wars.
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.
It could be some rogue ninjas who were against the peace treaties after the war. They might form a group and try to disrupt the newly - established peace in the ninja world.
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.
Sasuke could be an alternative. He has strong ninja skills and a deep understanding of the ninja world. His experiences have made him grow into a very capable person, and his Sharingan gives him an edge in combat and strategic planning.
One reason could be that there are political forces against him. Maybe some of the elders in the village don't trust his unorthodox ways and fear he'll bring too much change. Another could be that there are other candidates who seem more suitable on the surface, perhaps someone with a more traditional shinobi background who doesn't have Naruto's wild streak.
Well, it could be that Naruto meets the Hokage in a different time - space. They might work together to change some important events in the history of the village. For example, preventing a great disaster or changing the fate of some important characters. And Naruto could learn a great deal from the Hokage's wisdom and leadership in this encounter.
There could be a focus on Naruto learning new forms of the Rasengan. Hokage Naruto, with his vast experience, could teach Naruto different ways to infuse the Rasengan with other elements more easily. Maybe Naruto would learn how to quickly switch between a Fire - Rasengan and a Wind - Rasengan during combat.
In many fanfictions, one challenge is dealing with internal political unrest. There are often clans in Konoha who may not fully support Naruto's new ideas as Hokage. Another challenge could be external threats from other villages that see Naruto's new leadership as a potential threat to their own power.
Even Naruto himself could be a subject of this 'evil Hokage' concept in fanfiction. Maybe he is possessed by some dark entity or has a major change of heart due to some extreme event. This would completely change his character and turn him into an evil Hokage, which would be a very interesting and unexpected twist.
One possible plot could be that Naruto is somehow transported to a different timeline where he has to fight the Hokage for a misunderstanding. Maybe there's a villain who has manipulated events to make the Hokage think Naruto is a threat. So Naruto has to fight not only to prove his innocence but also to save the village from the real danger that the villain poses.
Maybe Naruto has always idolized the Hokage in secret. He could be studying the ways of past Hokages on his own, trying to learn their leadership skills and jutsu. For example, he might be secretly practicing Minato's Flying Thunder God Technique because he admires his father so much.