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.
Another possibility is a dark entity that is awakened by Naruto's arrival. This entity could be something that was sealed away long ago in Hogwarts, and Naruto's unique chakra or energy breaks the seal. It then starts causing chaos and destruction, and Naruto has to team up with the Hogwarts students and teachers to stop it.
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 a dark wizard who has infiltrated Hogwarts under a disguise. Percy might be the one to first suspect this wizard's true identity.
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.
It could be the village elders. In the original series, they often made decisions behind the scenes. In a 'naruto goes rogue' scenario, they might be the ones who push Naruto to the edge. For instance, they could be plotting against him to maintain their power in the village.
Maybe Danzo could be the main antagonist. He has always been a bit of a shady character in the Naruto series. He could see Naruto as a threat and use his influence to frame him and send him to prison to further his own political or power - hungry goals.
Maybe a new character could be introduced as the main antagonist. A powerful goth - like ninja from a far - off land who is jealous of Naruto's newfound dark power. This character could have a similar set of skills as Naruto but with a more malevolent intention. He might try to steal Naruto's power or defeat him to prove his own superiority in the goth ninja world.
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.
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.