Well, it could be a dark wizard in disguise. This dark wizard could be using Hermione as a pawn in a bigger plan. By making it seem like she's sabotaging homework, he hopes to create chaos in Hogwarts. He might be secretly influencing Hermione's actions or directly interfering with the homework to make it look like she's at fault. Another option is a disgruntled house - elf who is tired of seeing Hermione always doing so much work and decides to play a trick on her by making it seem like she's sabotaging the students' homework.
The antagonist could be a magical creature that has infiltrated Hogwarts. Maybe it's a mischievous imp that targets Hermione because it senses her strong magical aura. The imp then causes the homework sabotage and tries to make it look like Hermione is responsible. Or it could be an older student who feels threatened by Hermione's academic success and decides to set her up by making it appear she's sabotaging homework.
One plot idea could be that Hermione accidentally sabotages everyone's homework when she tries a new spell to organize it. The spell backfires and scatters all the answers. Another could be that she is framed for sabotaging homework by a jealous classmate who wants to get her in trouble. Or perhaps Hermione sabotages her own homework as a form of self - imposed stress relief, realizing she's been too much of a perfectionist.
Another possibility is an ancient evil that has been awakened. This entity might see Hermione as a threat because of her potential power. So it curses her to stop her from growing stronger. In this case, the antagonist would be very powerful and mysterious, and Hermione and her friends would have to do a lot of research and exploration to find a way to defeat it.
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.
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.
It could be Draco Malfoy. In some fanfictions, Draco might be pushed to such an extreme by his family's beliefs that he resorts to physical violence against Hermione. He might punch her out of jealousy or to assert his so - called superiority.
Voldemort could be the antagonist. Even if he was defeated in the original story, there could be a scenario where some remnant of his dark magic causes Harry and Hermione to disappear. Maybe he had a secret plan that was set to activate after his death and it involved taking them out of the picture.
It could be a jealous student who wants to undermine Hermione's intelligence. They might have cast the spell to turn her into a baby thinking it would be a great way to get her out of the way. This student could be someone who is always overshadowed by Hermione in class and exams.
It could be a power - hungry student who wants to undermine Hermione and Favo Prefect. This student might be jealous of their status as prefects and the respect they get from teachers and students alike. So, they try to create problems for them, like spreading false rumors or sabotaging their projects.
It could be an old and powerful vampire who sees Hermione as a threat to his rule. Since Hermione is a very intelligent witch - now vampire - she might be able to figure out a way to undermine his power.
It could be an old muggle acquaintance who is jealous of Hermione's success in the wizarding world. Maybe they sense that she's different and are determined to find out her secrets and expose her.