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.
Well, 'Naruto meets Pain: The Alternate Ending' is a cool fanfic. In this story, Naruto uses a completely different strategy when facing Pain that we don't see in the original anime. It makes for a very exciting read. There's also 'Naruto and Pain: A Reconciliation' which explores what would happen if Naruto managed to convince Pain to change his ways much earlier in their encounter.
There's also 'The Bond of Enemies'. In this fanfic, Pain, after his defeat, is given a second chance at life by Naruto. It shows a really interesting dynamic as Pain tries to figure out his new place in the world with Naruto's influence. It has some great action scenes and emotional moments.
It could be about Naruto having some sort of connection to Pain. Maybe in this fanfiction, Naruto is somehow related to Pain in a way that wasn't in the original story, like being his son in an alternate universe. This could lead to a whole new set of storylines, with Naruto perhaps having to deal with the legacy of Pain while also following his own path as a ninja.
A prevalent theme could be the power of the human spirit. Despite experiencing pain, Naruto's spirit is strong enough to convert that pain into a formidable power. This can also be related to the theme of hope. His transformation from pain to power gives hope to other characters in the fanfiction that they too can overcome their own pain and grow stronger.
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.
Hinata saving Naruto from Pain in fanfiction can take on many forms. It could be that Hinata has been secretly training and has a new set of abilities that she unleashes to save Naruto. This not only changes the course of the battle but also the dynamics between the characters. Fanfic writers might also add some emotional elements, such as Hinata's inner thoughts and feelings during the rescue. This makes the story more engaging and gives readers a fresh perspective on the Naruto - Hinata relationship.
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.
A fanfiction titled 'Naruto's Admiration for Pain' is also worth checking out. It focuses on Naruto's growing admiration for Pain's power and ideology. However, Naruto also tries to change Pain's more extreme views. The story is full of intense dialogues and Naruto's internal struggles.