Cinder Fall could also be the main antagonist in this case. She has a history of targeting Ruby and her friends. Maybe she devises a new plan to get rid of Ruby once and for all by making her disappear, either by using her own powers or by manipulating others.
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.
It could be Adam Taurus. He's a well - known and very radical member of the White Fang in the RWBY universe. His extreme views and violent methods would put him directly at odds with Ruby's more peaceful and inclusive approach.
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 a powerful Grimm - like being that has evolved beyond the normal Grimm. This antagonist might have the ability to think and strategize like a human, making it a much more dangerous foe for Ruby and her team. It could be leading the Grimm attacks in a more organized way, targeting specific areas to cause maximum chaos.
There's a possibility that a new character could emerge as the main antagonist. Ruby's time - traveling could disrupt the normal flow of events, and this might create a new power - hungry or revenge - seeking character. This new antagonist could be someone who blames Ruby for the changes in the timeline and wants to stop her at all costs.
It might be Salem. Since Ruby's silver eyes are a major threat to her plans, an early activation could draw Salem's immediate attention. She would then send her most powerful minions to deal with Ruby.
If Ruby turns evil, she could become her own antagonist in a way. Her former self, the Ruby that was good, could be seen as what she is now fighting against. Her friends would also become antagonists as they try to stop her from causing more harm.
Perhaps it could be an evil version of one of Ruby's own relatives. Like an alternate version of her father or mother who has been corrupted by some dark force. They would then raise Ruby with their evil values, making her believe that what they do is right and leading her down a dark path.
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.
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.
The main antagonist could also be a new character created specifically for the fanfic. This character could be an ancient evil that has been waiting for an opportunity to corrupt a powerful Huntress like Ruby. They would then use Ruby's newfound evil nature to further their own dark plans, and Weiss, Blake, and Yang would have to face both Ruby and this new threat.