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.
A third possibility is a group of rogue Huntsmen who have turned to the side of the Grimm. They believe that the current system of fighting the Grimm is flawed and that by siding with them, they can create a new order. Ruby would have to not only fight against these Huntsmen but also try to convince them that their actions are wrong and that the Grimm are not to be trusted.
There could be an ancient Grimm entity that has been dormant in the Pacific for ages. Due to some recent events, it wakes up and starts wreaking havoc. It has the ability to corrupt other Grimm and make them more powerful and intelligent. This entity would be a formidable antagonist for the RWBY team as they try to stop its reign of terror in the Pacific region.
It could be a rogue Huntsman who wants to use Ruby's power to control Grimm for his own evil purposes. He might believe that with the Grimm under his control, he can rule over Remnant. He would then be constantly trying to kidnap Ruby or figure out the secret behind her power, and would oppose team RWBY at every turn.
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.
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.
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 someone from Ruby's world who doesn't like the idea of her training an outsider like Naruto. Maybe a powerful mage or a warlord who sees Naruto as a threat to their power or the balance of their world.
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.
Yes, there might be. The 'RWBY' fandom is quite large and diverse, so it's not surprising that there could be a fanfiction with such an interesting concept as Ruby being part Grimm. It could explore a whole new side of her character and the story's lore.
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.
Another option could be a group of pirates who believe that the Ruby of the Sea can lead them to a great treasure. They constantly try to capture the Ruby and the Jester has to fend them off to protect her. The pirates would be a constant threat throughout the fanfic.