Perhaps it could be a Death Eater who has escaped from Azkaban and is looking for a way to get back in Voldemort's good graces. He hears that Harry Potter is staying at the Dursleys' and decides to attack him while he's alone, thinking it would be an easy victory and a great gift to bring to Voldemort.
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.
The main villain could be an escaped criminal who stumbles upon the house thinking it would be a good place to hide. But when he realizes there's a kid alone, he decides to take advantage and ransack the place. The kid has to use his wits and the resources around the house to defeat this dangerous villain.
Well, perhaps in this fanfiction, Harry discovers a secret room in the Dursleys' house when he's home alone. Inside, he finds a magical object that was left there by a previous wizard who used to live in the area. This object has the power to transport him to different places in the wizarding world for a short time. But he has to be careful because every time he uses it, it sends out a signal that attracts dark creatures. So he has to deal with these threats all by himself while also trying to figure out how to control the object.
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.
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.