One way to conceptualize a love story between Naruto and Pain could be through the idea of redemption. Naruto might see the pain and confusion in Pain's heart that led him to his extreme actions. He could strive to show Pain a different path, and in this process, a deep connection could form that might turn into love. Naruto's unwavering belief in the goodness of people could gradually break down Pain's walls.
The biggest obstacle would be their conflicting ideologies. Naruto believes in the power of friendship and forgiveness to bring peace, while Pain believes in using force and instilling fear. It would be very difficult for them to overcome this fundamental difference in their worldviews and come together in love.
Well, in the original Naruto story, Pain's actions are somewhat more straightforwardly presented as villainous. But in the fanfic, it might humanize Pain more. It could show his past traumas and how they led him to his extreme beliefs and actions.
One common theme is the struggle for acceptance. Female characters often face discrimination in the Naruto world, and this can cause a great deal of emotional pain. They have to fight not only external enemies but also the prejudices within their own communities.
I'm not sure specifically as there could be many different takes in a fanfic with that title. It might be about a character in Naruto who endures some sort of unending pain, perhaps related to their past traumas, like Naruto himself who has the pain of being an orphan and ostracized for so long. Or it could be about a villain like Sasuke who has his own internal pain that never seems to go away.
One possible plot is that Pain targets Hinata to get to Naruto. Since Hinata has a special place in Naruto's heart, Pain might think that by hurting her, he can break Naruto. But Hinata shows great courage and Naruto comes to her rescue.
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.
One unlikely ally could be Zetsu. Zetsu is usually seen as a villain, but in a fanfic, he could have his own motives for helping Naruto defeat Pain. Maybe he wants to disrupt the Akatsuki's plans from the inside and sees Naruto as a useful tool for that.
Another reason could be related to his relationships. Maybe in a fanfic, Naruto has a falling out with his friends like Sasuke or Sakura. This emotional hurt can be just as painful as physical harm. The author might use this to show how Naruto grows and overcomes such internal struggles.
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.