Maybe it could be a new character who is a combination of ninja and wizardry evils. This character could be jealous of Naruto's unique abilities that bridge the gap between two different worlds and wants to stop Naruto from uniting the ninja and wizarding communities against him. They could have powers that are a mix of dark magic and some dark ninja jutsus.
It could be Voldemort if the story takes place during the time he was a threat. Naruto's arrival might disrupt his plans in some way, so he would see Naruto as an obstacle.
It could be a new dark wizard who has been lurking in the shadows. Maybe someone who was once a student at Hogwarts but turned to the dark side.
It could be a dark wizard who has infiltrated Hogwarts under a disguise. Percy might be the one to first suspect this wizard's true identity.
The main antagonist could be Naruto himself in a sense. Since he has gone insane, his actions are now unpredictable and harmful to the people around him. His former friends, like Sakura or Kakashi, might have to step up and try to stop him, seeing him as the new threat.
The Hidden Leaf Village itself could be the main antagonist. If they turn on Naruto for no good reason, they become the force he has to fight against as a rogue ninja.
It could be Danzo. He's always been a bit of a shady character in the Naruto series. He might see Naruto as a threat to his power and influence in the village. So, he could frame Naruto for some crime and get him sent to jail just to eliminate his competition.
Naruto would obviously be one of the main characters. And for the Hogwarts side, it could be Harry Potter himself. Imagine Naruto and Harry having a unique connection that develops into a yaoi relationship. They both have a sense of justice and a willingness to fight for what's right, which could be the basis for their relationship.
Another possibility is that there is a rogue ninja in Kumo who uses Naruto's neglected state to his advantage. He might try to manipulate Naruto into doing things that would be bad for both Naruto and Kumo, all while remaining in the shadows and making it seem like Naruto is acting on his own accord.
Maybe a rogue ninja who has made a pact with a dark wizard in Hogwarts could be the main antagonist. This ninja - turned - villain has combined his ninja techniques with dark magic and is causing havoc in Hogwarts. Naruto would be sent to stop him, but he'd face a tough challenge as this antagonist knows both the ways of the ninja and the secrets of Hogwarts magic.
Another possibility is Madara Uchiha. Even if he is not fully alive in the original story, in this fanfiction, his spirit or some form of his influence could be present. He could manipulate Naruto's new evil state for his own ends, like trying to destroy the ninja world that he once had a vendetta against.