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 the main antagonist is actually a corrupted member of the Hidden Leaf's own leadership. They manipulate situations to make Boruto look like a threat, which in turn makes Boruto go rogue. This antagonist could be trying to cover up their own misdeeds within the village and sees Boruto as an obstacle.
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 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.
In the 'Boruto goes rogue fanfiction', it could be that he discovers a dark secret about the village leadership. This makes him lose faith in the system and go rogue. He might then seek out other outcasts or those with similar grievances to form his own group to oppose the village's unjust ways.
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.
Lex Luthor could be a great antagonist. He might see Rogue Lemon as a new variable in his plans to defeat Superman. He could try to manipulate Rogue Lemon into turning against Superman or use her powers for his own evil purposes.
The Joker could be the main antagonist. Even though Batman is in jail, the Joker could find a way to continue his chaos - making. He might try to get into the prison to torment Batman or use the situation to his advantage by causing mayhem in Gotham City without Batman there to stop him.
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.
A powerful sorcerer could be the main antagonist. He might be after Percy's powers or trying to use the school as a base to spread chaos. Maybe he wants to open a portal to the underworld right in the middle of the schoolyard.
Perhaps a new, powerful demigod - vampire hybrid that Percy has to face. This hybrid could be causing trouble in Forks, and Percy has to stop it before it destroys the delicate balance between the vampires, werewolves and humans there.
There might be a character who is secretly from the wizarding world but has turned to the dark side. This character could be after Harry in the Ouran setting, trying to use the chaos of the new environment to their advantage to get to Harry without being noticed by the Hogwarts professors.