A group of Death Eater sympathizers within the Ministry could be the main antagonists. They still hold onto the old pure - blood supremacist ideals and see Hermione, a Muggle - born witch, as a threat. So they fabricate evidence against her and send her to Azkaban to send a message to all Muggle - borns that they are not welcome in the new wizarding order they are trying to create.
Maybe it's a new dark wizard or witch who has infiltrated the Ministry. They manage to manipulate the situation so that Hermione is blamed for their own misdeeds and sent to Azkaban. Their goal could be to cause chaos in the wizarding world and Hermione was the only one who could stop them.
It could be a corrupted prison guard. They might be taking advantage of the chaos in Azkaban to carry out their own evil plans, like stealing magic from the prisoners. Harry would have to stop them while also dealing with his own situation in the prison.
One possible plot could be that Hermione is wrongly accused of a serious crime against the wizarding world, perhaps a dark magic related offense that she didn't commit. As a result, she is sent to Azkaban. Inside Azkaban, she has to deal with the Dementors and the harsh prison environment. Meanwhile, her friends Harry and Ron believe in her innocence and start to investigate to find the real culprit and clear her name.
One possible plot could be that Hermione discovers a dark secret about Azkaban. And the Ministry of Magic, fearing she'll expose it, sends her there. In Azkaban, she meets some other wrongly imprisoned witches and wizards. Together, they plan an escape while also trying to expose the real criminals in the wizarding world.
One possible plot could be that Harry is wrongly accused of a serious crime within the wizarding world and is sent to Azkaban. There, he discovers a dark secret about the prison itself, like there being a hidden force controlling the Dementors. He has to use his skills and the loyalty of his friends to expose this secret and clear his name.
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 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 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.
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.