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.
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.
Sasuke is often a popular character in these fanfics. His own stint as a sort of rogue ninja makes him a natural fit. Also, Orochimaru, who was a rogue ninja for a long time, is frequently included. He has a lot of mystery and power associated with him.
Kakashi could also be the main character in a different take on 'naruto rogue ninja fanfiction'. Imagine if for some reason, Kakashi was framed as a rogue ninja. He would have to use his intelligence and combat skills to clear his name while also dealing with the challenges of being an outcast. He might even discover some dark secrets about the Hidden Leaf Village in the process.
The Leaf Village authorities could be the main antagonists. Since Naruto is now considered a rogue, they would be the ones trying to hunt him down. They might see him as a threat to the village's stability and security.
Well, one interesting plot could be Naruto's struggle to survive in a world that now sees him as a rogue. He might have to constantly evade capture from his former friends and allies. Another could be his journey to find out who framed him as a rogue in the first place.
One interesting plot could be a rogue ninja who discovers a hidden power within themselves that was suppressed all along. This new power makes them a target for both their former village and other rogue elements. Another plot might involve a rogue ninja forming an unlikely alliance with other outcasts to take on a greater evil that threatens the ninja world.
In a 'naruto becomes a rogue ninja fanfic', it could start with Naruto being ostracized by the village due to his growing power which some elders fear. They try to suppress him, and Naruto, feeling betrayed, decides to leave and become a rogue ninja. He then might go on a journey to find a new place where he can be accepted for who he is, and along the way, he could meet new allies and enemies alike. He may also develop new jutsu away from the traditional teachings of the village.