Often, Naruto's relationships with other characters are explored further. He might have deeper conversations with Sasuke, trying to convince him to come back to the village for good. His bond with Sakura could also develop in different ways, perhaps becoming a stronger friendship or even something more romantic in some fanfictions.
In some fanfictions, after Naruto defeated Pain, the village started to rebuild immediately. Naruto became a hero not only in name but also in the hearts of every villager. People looked at him with newfound respect and admiration.
The Akatsuki remnants could still pose a threat. Members like Sasori or Deidara might have had backup plans or followers who now want revenge for the Akatsuki's downfall. They could target Naruto specifically, seeing him as the one who brought down Pain and disrupted their plans.
One possible plot could be that the village, still shaken by Pain's attack, blames Naruto for not preventing all the destruction. They think he has some hidden connection to Pain and turn on him. Naruto, heartbroken, decides to leave the village and find out the truth about his past and the Akatsuki on his own.
Maybe Orochimaru's former followers who are still lurking in the shadows. They see Naruto as a threat and Hinata as an easy target to get to Naruto. Another possibility could be some power - hungry shinobi from other villages who view Konoha as weak after the Pain incident. They might target Naruto and Hinata as key figures in Konoha's future to try and undermine the village's rebuilding efforts.
One possible plot could be that Hinata and Naruto start to train together more intensively. After facing Pain, Naruto realizes Hinata's feelings for him more deeply. They could go on missions side by side, and Hinata becomes stronger under Naruto's influence. Naruto, in turn, starts to see Hinata as not just a friend but someone he could potentially have a future with.
In many fanfictions, after the Pain arc, Naruto and Hinata's relationship often deepens. Naruto starts to see Hinata in a new light. He realizes her strength and her unwavering feelings for him. This can lead to more interactions between them, like Naruto becoming more protective of Hinata and Hinata being more confident in expressing her love for Naruto.
He'll likely lose his power and influence in the village. Once Naruto reveals his secrets, the villagers won't trust him anymore. His actions might be put on trial, and he could be exiled from the village.
Another development could be that Naruto starts to understand the world outside the Hidden Leaf better. His encounter with Pain, who had his own ideology about peace, makes Naruto question his own views. So, he might embark on journeys to other villages to learn more about different cultures and ways of achieving peace, which in turn changes his perspective on many things.