There is a chance that an ancient and powerful dark wizard, who has been in hiding, resurfaces and wants to disrupt the peace in the wizarding world. Hermione is trying to stop him, but he is too clever and frames her for his own dark deeds, leading to her imprisonment in Azkaban.
Maybe a jealous wizard or witch within the Ministry of Magic. They might be envious of Hermione's popularity and influence among the younger wizards. So they fabricate evidence against her to get her locked up in Azkaban.
There could be a group within the Ministry of Magic itself that is corrupt. They might not like Hermione's progressive ideas about the treatment of house - elves and other non - human magical creatures. So they conspire to put her in Azkaban to silence her and maintain the status quo.
Well, perhaps in the fanfiction, Hermione is wrongly accused of a serious crime like dark magic use. Maybe some powerful and corrupt wizarding figure wants to silence her for her Muggle - born rights activism. So they frame her and she gets sent to Azkaban.
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.
Harry Potter, of course. His friendship with Hermione is a crucial part of the original story, and in a fanfiction, their bond can be explored even deeper. Maybe Harry discovers a new side of Hermione during the events of Prisoner of Azkaban.
One possible plot could be that Hermione was wrongly accused of a serious crime against the wizarding world. Maybe she was framed by a dark wizard who wanted to silence her for her intelligence and knowledge. She might be struggling to prove her innocence from within Azkaban while her friends on the outside, like Harry and Ron, are desperately trying to find evidence to free her.
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.
Harry Potter is an obvious choice. Given their strong friendship and the many adventures they've had together, Harry would surely do everything in his power to rescue Hermione. He has faced many challenges before and wouldn't stand by while his friend is in Azkaban. Another likely character is Ron Weasley. He and Hermione have a complex relationship, but he would definitely not let her rot in Azkaban. Ron has his own skills and resources within the wizarding world that he could use to plan a rescue. Dumbledore, if he were still alive in the fanfiction, would also be a likely rescuer. He was always one to see the good in people and Hermione's intelligence and value to the wizarding world would make him want to save her. He has the power and influence to challenge the decision to send her to Azkaban.
Another possibility is a jealous student at Hogwarts. There are always students who might be envious of Hermione's academic achievements. They could set up a prank or a trap that goes wrong and ends up hurting her. For example, a student who is tired of Hermione always getting the top grades in Potions might tamper with her cauldron during a class experiment, resulting in an explosion that hurts her.
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.
One consequence could be a change in the public's perception of Hermione. Some might see her as a hero for standing up against an unjust imprisonment, while others might view her actions as traitorous, especially if they believe Draco was truly guilty. This could create a divide among the wizarding community.