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.
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.
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.
Well, it could involve Ruby being influenced by an evil force in this fanfic. Maybe she's taught dark magic or has her moral compass twisted. For example, she might start seeing the world in a more cynical way and use her powers for less noble purposes.
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.
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.
Maybe it's a mysterious figure from Ruby's family's past. Someone who had a connection to her mother or father and felt a sense of duty to raise Ruby. This would add a layer of mystery and family drama to the fanfiction.
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.
I'm not sure specifically as there could be many different takes in such a fanfiction. It might involve Ruby growing up under Cinder's influence, which could lead to a complete change in her character, values, and fighting style. Maybe Cinder has some ulterior motives for raising Ruby, like using her as a weapon or a pawn in her grand scheme against Beacon Academy and the other Huntsmen and Huntresses.