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.
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.
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 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.
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.
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.
In a 'naruto goes rogue' fanfic, the plot could involve Naruto feeling betrayed by the Hidden Leaf Village. Maybe he discovers some dark secrets about the village leaders. For example, he might find out they were using him all along. So, he decides to break away and form his own group of outcasts who also felt wronged by the village.