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.
There's a chance that the Dementors themselves are, in a way, the main antagonists. In the fanfiction, they could be acting under some external influence or their own dark desires. They make Hermione's life in Azkaban miserable and try to drain her of her positive emotions as she tries to prove her innocence.
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.
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 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.
Perhaps a new dark wizard or witch who has infiltrated the Ministry of Magic and made sure Harry was sent to Azkaban. This antagonist could be working towards a bigger plan to take over the wizarding world and sees Harry as a major threat even when he's locked up.
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.
Perhaps a powerful magical being from a different realm is the antagonist. This being might mistake Hermione for someone else or see her as a key to something in the wizarding world. So, it uses its magic to make her disappear. This being would be very difficult to defeat or negotiate with, making it a huge challenge for those trying to find Hermione.
Another possibility is a dark wizard or a group of dark wizards who are after some powerful magic that the Lestrange family has, and Hermione gets in their way as she tries to protect the family or uncover the secrets. They would be the main force that Hermione has to face and overcome throughout the fanfiction.
Obviously, Harry Potter himself is the central character. Hermione and Ron would most likely be involved too. They would probably try to find a way to get Harry out of Azkaban. Dumbledore might also play a role, perhaps guiding Hermione and Ron from behind the scenes or even trying to influence the wizarding court to re - evaluate Harry's case.
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.