A new dark wizard or witch could be the villain. Maybe they are jealous of Harry's fame and power. They study dark arts intensively and develop a spell to trap Harry in his mind. This new villain might not be directly related to Voldemort but has their own evil motives, like ruling the wizarding world by getting rid of Harry who is seen as a major obstacle.
Well, in this kind of fanfiction, it might be that a new, unknown enemy has developed a mind - trapping curse specifically for Harry. This enemy could be someone who wants to use Harry's knowledge of the wizarding world for their own evil purposes. So they trap him in his mind to extract information. Also, it could be related to some side - effects of a powerful magic Harry was trying to use. For example, if he was trying to access some deep, forbidden magic, it backfired and trapped him in his own mind.
Perhaps it's an old enemy that was thought to be defeated. This enemy might have been biding their time and finally finds a way to get revenge on Harry by driving him mad. It could be a Death Eater who was overlooked or a creature from the Forbidden Forest with a grudge.
In this fanfiction, it could be that the pressure of being 'The Chosen One' finally gets to Harry. All the battles, the losses he has endured, and the constant threat of Voldemort might push him over the edge. He could start acting erratically, pushing away his friends and allies because he no longer trusts his own judgment.
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.
Quirrell could be the main villain. He was already under Voldemort's influence in the original story. It's possible that in this fanfiction, he doesn't hold back and attacks Harry more directly and lethally during his first year. Maybe he uses his position as a teacher to get close to Harry and then strikes when he has the chance.
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.