Maybe a new and powerful criminal organization. They see Naruto as a threat when he's still in the village, so they frame him, causing him to go rogue. Then they become the main antagonists as they try to eliminate him before he can expose their plans.
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 an old enemy of Naruto who has now risen to power within the village. This person manipulates the situation so that Naruto is forced out of the village and becomes a rogue. And then this enemy continues to hunt Naruto down to finish him off once and for all.
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.
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.
It could be a new character, someone who has a vendetta against Boruto and drives him to go rogue by framing him for various crimes. This new antagonist might have their own motives related to taking over the Hidden Leaf or causing chaos in the shinobi world.
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.
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.
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.
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.
It could be one of the dark mages from the Mahou Negima Sensei world who sees Naruto as an intruder and a threat to their plans. Maybe they want to steal his chakra for their own dark magic purposes.
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.
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.