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.
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 Salem. She has always been interested in the power of the silver eyes, and Ruby having those eyes makes her a prime target. Salem might send her minions to kidnap Ruby, which would lead to her disappearance.
A group of rogue demigods could be the main antagonists. They believe that Percy is too powerful and his presence is causing more problems than solutions in the demigod world. So they make him disappear. But when Percy comes back, he shows them that they were wrong and that they have been mislead by false beliefs.
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.
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.