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.
In fanfiction, the Rinnegan is often depicted as more powerful than the Sharingan in many ways. The Rinnegan has abilities like the Six Paths techniques which can be extremely overpowered. For example, it can allow the user to control gravity, summon large creatures, and even revive the dead. While the Sharingan has its own set of cool abilities like predicting movements and casting genjutsu, it seems limited in comparison when it comes to the grand scale of power shown by the Rinnegan in most fanfictions.
In a fanfiction, the aliens could capture Naruto and try to study his unique abilities. The monsters then decide to rescue him because they realize his powers could be the key to defeating the aliens once and for all. The story could involve a lot of action as the monsters infiltrate the alien base to save Naruto.
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.
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.
In this fanfic, it might also re - imagine the battles involving Pain. Instead of the battles being just about physical combat, it could explore the psychological warfare aspect more. Pain's abilities, like the Six Paths of Pain, could be used in more creative ways to create a more engaging and different story. It could also focus on how the other characters in Naruto try to understand and counter Pain's complex ideology while dealing with the destruction he causes.
Archive of Our Own (AO3) is also a great place. It has a well - organized tagging system. Just search for 'Naruto' and 'Pain' tags and look for the ones that imply Naruto having positive feelings towards Pain. There are often some really creative works there.
Here's how a fanfic might go. After the battle with Pain, Naruto is surrounded by people, but his eyes keep searching for Hinata. When he finally spots her, he makes his way through the crowd. Hinata is blushing but stands her ground. Naruto reaches her and says, 'Thank you for always being there for me.' Then, he cups her face and kisses her. This kiss is a culmination of all the times Hinata has supported Naruto, and now he's finally realizing his own feelings for her.
In fanfiction, when Naruto gets injured by Pain, it could also trigger some new powers or abilities within Naruto. Maybe the injury acts as a catalyst for him to tap into a deeper level of the Nine - Tails' chakra. His injury might also make the other villages more aware of the threat that Pain poses. They could decide to form alliances with Konoha in order to deal with the Akatsuki as a whole. This would change the political landscape in the Naruto world.