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.
Sakura's relationship with Sasuke would likely change drastically. With Naruto gone, Sakura might turn to Sasuke even more for support, which could either bring them closer together or cause more friction as Sasuke may not be able to handle her grief. Kakashi, on the other hand, would be deeply affected. He might become more withdrawn, blaming himself for not being able to protect Naruto.
One possible plot twist could be that Naruto's death at Pain's hands leads to a dark turn in the Hidden Leaf. The villagers, in their grief and anger, start to question the ninja way and some might turn to darker methods of revenge. For example, Sasuke, upon hearing the news, could completely abandon any hope of redemption and go on a full - out rampage against the Akatsuki.
Konan could be really interesting. In some fanfictions, she might have a different backstory or motivation that affects the Naruto vs Pain fight. For example, she could be secretly trying to stop Pain from going too far in his destruction of the Leaf Village.
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.
It could be a random civilian. This would show Naruto the impact of the ninja world's violence on ordinary people, making him more determined to protect the innocent.
Well, Naruto is obviously one of the main characters. He's the one who's going to be doing the beating. And Pain is also a main character in this context, as he is the opponent Naruto has to defeat.
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.