Some rogue ninja from other villages might be the ones. They could see Kakashi as a symbol of the Hidden Leaf's strength and think that by torturing him, they can demoralize the village. Also, a new and unknown enemy created specifically for the fanfiction could be the torturer, with their own motives like wanting to steal Kakashi's knowledge of ninja techniques.
There could be a corrupt Hogwarts teacher who has been secretly practicing dark magic. This teacher, perhaps a Potions or Defense Against the Dark Arts teacher, has been influenced by the allure of power. They see Harry as a threat to their new - found power and decide to torture him in the Great Hall to send a message to the other students that they are in charge now.
Perhaps it's an organization that wants to use Kakashi for their own evil plans. They might think that Kakashi's skills and knowledge would be useful for them. For example, they could be trying to create some sort of super - weapon and they need Kakashi's expertise in ninjutsu.
It could be the dominant character in the yaoi pairing. If there is a strong - willed character in the relationship, they might take it upon themselves to punish Kakashi for interfering or causing trouble.
It could be an original character created just for the fanfiction. Maybe a mysterious ninja woman who crossed paths with Kakashi during a mission and they had a brief but intense relationship.
Maybe an organization that wants to use her unique abilities. If she has inherited some special power from Kakashi or has her own distinct skills, an evil organization could try to capture her and force her to work for them. They would be the main obstacle she has to face in the story.
Perhaps an old enemy of Naruto's who resurfaces and decides to target his family. This could be someone who was defeated by Naruto long ago but has now grown stronger and wants to cause harm to his loved ones. They might also see Kakashi as a threat in protecting the family.
It could be Orochimaru. He might be interested in the unborn child for some dark experiment, thinking that the child of Kakashi and Rin could possess some unique abilities. He could send his minions to spy on them or even try to kidnap Rin.
It could be Orochimaru. He might see the baby versions of Team 7 as perfect subjects for his experiments. He could try to kidnap them to use their unique chakra or potential for his own dark purposes.
Naruto would likely be involved. He has a strong bond with Kakashi and would surely try to rescue him. Sasuke could also be part of the story. Given his relationship with Itachi, it would add an interesting dynamic.
Well, for Dark Kakashi crossover fanfiction, Tumblr can be a useful resource. There are many fanfic writers and fans who post about their works or share links to great stories there. Also, some Naruto - focused forums might have sections dedicated to fanfiction. These often have users discussing and recommending different fanfics, including those with Dark Kakashi in crossovers. Just be sure to explore different threads carefully.