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.
In some fanfictions, there could be original characters created by the author. These characters might be servants in Lestrange's household along with Hermione, and they could either be friends or foes to Hermione in her situation as a slave.
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.
It could be the same group or person who tortured her in the first place. They might be trying to finish the job or silence her before she can expose their evil deeds.
Hades would be a likely main antagonist. He rules the Underworld and might see Hermione as a threat or an opportunity. If he thinks she has something valuable, like her knowledge of magic, he could try to keep her trapped in the Underworld. Or he might oppose her if she's trying to change something in his domain that he doesn't want changed.
It could be Bellatrix Lestrange. She's always been a cruel and powerful dark witch. In the fanfiction, she might have captured Hermione and bound her to the wall to torture her for information about Harry Potter or the Order of the Phoenix.
Voldemort himself could be the main antagonist in this scenario. He might offer Hermione something she desperately wants in exchange for her betrayal. Maybe he promises to spare her Muggle - born friends if she gives up the Order's plans and secrets. His powerful and intimidating presence could easily force Hermione into a difficult situation where she feels she has no choice but to betray.
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.