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.
Kakashi could become more distrustful after meeting Tobi. Since Tobi is such a mysterious figure, Kakashi might start to suspect everyone around him more.
Naruto would probably be one of the first to try and rescue Kakashi. He has a strong bond with Kakashi and would not stand by while his teacher is in danger.
One possible plot could be that Tobi kidnaps Kakashi to gain some valuable information. Maybe he wants to know about the Sharingan secrets Kakashi has. Tobi could hold Kakashi in a secret lair and try to interrogate him.
One possible plot could be that Tobi, Sakura, and the female reader all end up on a mission together. Tobi's unpredictable nature might create some comical situations at first. Sakura, with her medical and combat skills, would be a reliable ally. And the female reader could have some unique abilities that help them overcome the challenges in the mission, like perhaps the ability to communicate with animals which gives them an edge in a forest - type mission.
The mystery surrounding the characters. Tobi is a very enigmatic figure, and Kakashi has his own secrets. When combined in fanfic, it creates a lot of intrigue.
One popular 'tobi x kakashi fanfic' could be 'The Unseen Bond'. It explores a unique relationship between the two characters, delving into their shared past and how their paths cross in unexpected ways. The story is filled with mystery and a slow - burn kind of connection.
Perhaps an organization that is trying to steal Sakura's medical knowledge for their own evil purposes. They view Tobi as a threat because of his combat skills and the fem reader as a potential source of information about Sakura. So they send their agents to target all three of them.
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.