It could be an alternate version of Dumbledore. Maybe in this universe, Dumbledore has been corrupted by power and his thirst for knowledge leads him to do dark things. He could be trying to control the entire wizarding world using some powerful and forbidden magic.
In an Alter Universal Fanfiction, the main villain could be a new character. Suppose there is a wizard who was once a student at Hogwarts but was expelled for practicing dark magic that was so new and different that it was not even known before. This wizard now wants revenge on the school and the wizarding world for his expulsion and has amassed a group of followers to carry out his evil plans.
In this fanfiction, it could be a group of corrupted magical nobles who oppose Harry's rule. They are used to having all the power in the alternate universe and don't want to give it up to an outsider like Harry. They could be plotting all sorts of schemes to undermine Harry, from spreading false rumors to outright attacking him and his supporters.
Well, it could be about Harry Potter finding himself in an alternate universe where he is a king. Maybe he has to deal with different magical politics and power struggles that are far more complex than in his original world. He might have to form new alliances and face new enemies all while trying to figure out how this new world's magic works compared to his own.
Well, in an Alter Universal Fanfiction, there could be a scenario where the Sorting Hat sorts students based on different criteria. For example, instead of sorting by courage, intelligence, etc., it sorts by potential for a new kind of magic. Also, Voldemort could be a hero in this alternate world. He might have been misjudged in the original timeline, and in this new universe, he uses his power to fight an even greater evil. Additionally, the houses in Hogwarts could have different alliances. Maybe Gryffindor and Slytherin form an alliance against a new threat.
It could be a new character created by the fanfiction author. Maybe a powerful wizard who was once shunned by the wizarding community and now wants revenge by stealing magic.
A dark wizard who has merged the dark arts with Wonderland's magic could be the main villain. He might have created some sort of dark Wonderland where all the creatures are under his control, and Harry has to break this control to restore balance.
Perhaps the main villain is actually a corrupted version of a well - known character. For example, if Hermione was somehow influenced by the dark magic associated with the runestone path and turned against Harry. It would be a very unexpected and heart - wrenching twist, as she has always been such a loyal friend. But the power of the runestone path could be so strong that it changes her fundamental nature.
Maybe a new character, a Muggle - born wizard who was shunned by both the Muggle and wizarding worlds. This character, out of bitterness, decides to combine Muggle technology and magic to create the droid army and rule over both worlds. He would see Harry Potter and his friends as the main obstacles to his grand plan.
It could be someone new, a dark wizard who has learned about Naruto's reincarnation and wants to use his power for evil. This new villain might try to manipulate Naruto into using his chakra in a wrong way. Or perhaps it could be a combination of Voldemort and some of Naruto's old enemies from his previous life who somehow find a way to merge their powers in the Harry Potter world.
Perhaps an old Hufflepuff alumni who has turned to the dark side. This person was once a great student but became corrupted over time. They return to Hogwarts with the intention of using the Hufflepuff house as a base for their dark plans. They manipulate the Hufflepuff students, taking advantage of their kindness and hard - working nature, and turn it into a means to an end for their evil deeds. Harry gets caught up in this as he tries to figure out who this mysterious villain is and stop their plans.
A possible main villain could be Voldemort who somehow gains knowledge of Naruto's world and uses it to his advantage. He could learn to use chakra and combine it with his dark magic. He might create some sort of hybrid minions that are part - Death Eater and part - ninja. This would make him even more powerful and a greater threat to both the wizarding world and Naruto's world.