A plot could revolve around the power vacuum left by Naruto. The Leaf Village is in disarray, and other villages start to make moves against it. Pain might realize that killing Naruto wasn't really what he wanted in the long run, as it led to more instability. Or maybe a character who was in the background in the original story steps up to try and fill Naruto's shoes. They struggle to gain the respect and power that Naruto had, while also dealing with the grief of his loss.
In a fanfic where Naruto gets killed by Pain, it's a dark turn of events. The story would then likely focus on how the remaining characters cope. For example, Kakashi might feel a great sense of guilt for not being able to protect Naruto. Hinata would be heartbroken. Moreover, the Nine - Tails would be left without a host, which could also lead to all sorts of problems. The ninja world would lose its most prominent symbol of perseverance and friendship, and it would be a very different world from the one we know in the original Naruto story.
Jiraiya could be a great addition. Since he was Pain's teacher, his presence could add a lot of depth to the story. He could offer insights into Pain's past and also help Naruto understand Pain better.
In a 'naruto after pain fanfic', Naruto is key. However, characters like Tsunade are important too. She can lead the medical and administrative aspects of the village's recovery. Then there are Naruto's friends like Kiba and Choji. They can help with the physical tasks of rebuilding, and also in the security patrols around the village to prevent any new threats.
Obviously, Naruto and Pain are the main characters. Naruto, the energetic and determined ninja from Konoha. Pain, on the other hand, is the complex antagonist with his own set of beliefs about peace through pain. Their interactions are likely to be the focus of the fanfiction.
Obviously, Naruto would be one of the main characters as it's about him being the son of Pain. Pain himself would also be a crucial character, even if he might not be physically present all the time. And characters like Sasuke, Sakura, and Kakashi would still likely play important roles as they are Naruto's friends and mentors in the original story and would have to interact with Naruto in this new, changed scenario.
In some fanfictions, Naruto's pain might manifest through his actions. For example, he could become withdrawn and isolate himself from his friends. This is because Naruto has always been a social person, so any deviation from his normal behavior could be a sign of his internal pain.
One possible cause could be his sense of failure. Naruto always wants to protect his friends and village, so if he fails in a mission or is unable to save someone, it can cause him great pain.
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.