Yes, it could be. It might offer a fresh perspective by making Harry into a super villain. This could explore darker themes and character arcs that are different from the original series, adding a whole new layer of complexity to the story.
One great 'Harry Potter villain fanfiction' is 'The Dark Lord Ascending'. It gives a really interesting take on Voldemort's rise to power, exploring his motives and the early days of the Death Eaters in a way the original books didn't fully cover.
Voldemort could still be a potential villain even in 'Harry Potter leader fanfiction'. Maybe he returns in a different form or has some followers who are still causing trouble while Harry is trying to lead the wizarding world into a new future.
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.
A powerful foreign dark wizard could be the main villain. He might have heard of the prophecy about Harry Potter and decided to steal him from the Dursleys. This wizard could come from a far - off land with different and more dangerous dark magic, and his motives could be to gain ultimate power in both his own land and the British wizarding world by controlling Harry.
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.