A theme that often comes up is his physical pain and how he endures it. This can be used to show his strength and tenacity. For example, in a battle - themed fanfiction, he endures great pain but still manages to fight for the sake of his village. Also, the theme of self - discovery through pain is common. As he experiences pain, he learns more about himself and his limits.
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.
The theme of sacrifice could also be present. Both characters are willing to sacrifice for their causes. In the context of a yaoi fanfiction, this could translate into sacrifices for each other. For example, Pain might sacrifice his original plans for world domination for Kakashi, or Kakashi might put his village - related duties on hold to be with Pain, exploring the lengths they would go for their relationship.
Another possible fanfiction could be centered around Kakashi's pain from his past traumas, like the loss of his father. It could show how these past experiences resurface when he faces a new threat in the village. The story could detail how he overcomes this pain by finally coming to terms with his past and using it as a source of strength.
Well, it could be about Kakashi finally finding Obito after a long search. Maybe Obito has changed a great deal, and Kakashi has to come to terms with this new version of his old friend. They might have a battle first due to their different paths, but then they start to talk and remember their past together, like their time as teammates in Team Minato.
The main characters are Takashi and Kakashi. Takashi might be an ordinary person thrust into an extraordinary situation where he meets Kakashi. Kakashi, on the other hand, is a complex character with a mysterious past. Their encounter could lead to a whole new adventure for both of them.
It could be that Takashi is a new recruit in a ninja - like organization where Kakashi is a trainer. At first, Takashi struggles to meet Kakashi's high standards, but with determination and Kakashi's guidance, Takashi improves. Their relationship develops from a strict teacher - student one to a more friendly and mutual - respect - based bond.
In this fanfiction, perhaps Kakashi and Tobi meet in a battle. Kakashi might initially be suspicious of Tobi's true identity. Tobi could be playing mind games with Kakashi, trying to throw him off his game.
One of the most unique 'Naruto meets Pain' fanfiction concepts is in 'Naruto meets Pain: The Reverse Roles'. In this story, Pain is the one trying to save the village and Naruto is the one causing destruction. It completely flips the original roles and makes for a thought - provoking read. Another is 'Naruto meets Pain: The Dream World' where their encounter takes place in a shared dream world, and the rules of that world change how they interact and fight.
I'm sorry, I don't have specific 'Pain x Kakashi' yaoi fanfiction to recommend directly. You can try searching on fanfiction - specific websites like Archive of Our Own (AO3). They usually have a wide variety of fan - created works including yaoi pairings.