Perhaps it could be a corrupted version of an existing character. For instance, a jealous student at Hogwarts who turns to the dark side and starts stealing magic to prove himself better than Harry. This character could have some in - depth backstory about feeling overshadowed and then decides to take drastic measures.
Another possibility is a long - lost relative of Voldemort. This character might be following in Voldemort's footsteps, believing that by stealing magic they can achieve ultimate power. They could have some connection to the dark arts that was passed down in the family and use it to carry out their evil plans in the fanfiction.
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.
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.
A possible main villain could be a dark wizard who has learned some of the criminal tactics from the Detective Conan world. He could be using both magic and devious non - magical schemes to cause chaos. For instance, he might use spells to steal valuable items and then use the underworld connections in Conan's world to sell them.
Maybe the main villain could be a corrupted Hogwarts professor. This professor could be secretly teaching dark magic to students and when Harry's child discovers this, they become the target. The professor wants to stop the child from revealing their dark secrets and will go to great lengths to do so, making them a formidable villain in the fanfiction.
A possible main villain could be an ancient sorcerer from the new dimension who has been awakened from a long slumber. He's enraged that the wizarding world has been interfering with his dimension's magic, and decides to take revenge on Harry Potter's world. He has powers that are unknown to the normal wizarding world, like the ability to control time in his dimension, which makes him a formidable foe.
It could be a rogue wizard who has a vendetta against the Dursleys for some reason and decides to attack when Harry is home alone. Maybe the Dursleys once unknowingly wronged this wizard's family, and he wants revenge.
It could be a new character that is a combination of a dark wizard and a Hollow. This creature would be able to use both dark magic and Hollow abilities. It would target both Hogwarts students and Soul Reapers. Ichigo and Harry would have to figure out its weaknesses, which would be a difficult task as it has powers from two very different universes.