One potential main antagonist could be a powerful borrower from another colony. This borrower might see Merlin as a threat because of his magic or because he doesn't follow the traditional borrower ways. He could try to drive Merlin out of Camelot or even harm the other borrowers who have befriended Merlin. Another option is a dark sorcerer who discovers Merlin's situation. The sorcerer might want to capture Merlin to use his magic for evil deeds, or perhaps to steal Merlin's unique borrower - magic combination for his own gain.
Well, it could be Agravaine. He's always looking for ways to gain power and influence in Camelot. If he finds out about Merlin as a borrower and the unique situation, he might try to use it to his advantage. He could either try to expose Merlin to gain favor with Uther or try to control Merlin and use his magic for his own dark purposes. Also, there could be a group of anti - borrower humans in the castle. They might be superstitious or just plain cruel and they could be the main antagonists as they try to hunt down Merlin and the other borrowers.
Morgana could be a great antagonist. She might see the Lady of the Lake as a threat to her own power and plans for Camelot. And she could try to stop any alliance between Merlin and the Lady of the Lake.
It could be an unknown sorcerer who has infiltrated Camelot. This sorcerer could sense Merlin's power during 'The Moment of Truth' and see him as a rival. So, he tries to frame Merlin for dark magic, causing chaos in Camelot and forcing Merlin to prove his true intentions while also dealing with this new threat.
A powerful dark wizard could be the main antagonist. He might be jealous of Merlin's natural magic abilities and the Philosopher's knowledge. He could try to disrupt their work, steal their research, or even harm them to further his own evil plans.
One plot idea could be Merlin, as a borrower, is discovered by Arthur. At first, Arthur is shocked but then becomes intrigued. He decides to protect Merlin from the other humans in the castle. Another idea is that Merlin, in his tiny form, uses his magic in new and creative ways to help the borrowers' community. For example, he could create miniature tools or defenses against predators. A third idea might be that Merlin has to go on a quest to find a magical item that can restore his normal size, all while facing the challenges of being so small in a big world.
Morgana could be a likely antagonist. She has been at odds with Merlin in the series and has her own motives and powers. She might see stabbing Merlin as a way to further her plans against Camelot or to eliminate a threat to her own power.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
In this fanfiction, the Church or religious authorities in Camelot could be the main antagonists. Vampires are often associated with the devil or evil in religious beliefs. So, they might see Merlin's transformation into a vampire as a sign of him being corrupted by dark forces. They would try to exorcise or destroy him, not understanding that he's still the same Merlin at heart, just with a different form and new powers.
The Batman Who Laughs could also serve as the main antagonist. He represents a twisted version of Batman, and his goal could be to infect all the Batverses with his madness. His knowledge of Batman's tactics and his own insanity would pose a huge challenge for the normal Batman as he tries to stop him from spreading chaos.
A new character created specifically for the fanfiction could be the main antagonist. For example, a powerful being from another dimension who is attracted to the chaos in Remnant caused by the combination of RWBY and Starkiller's presence. This character could have abilities that are a threat to both Starkiller and the RWBY characters, forcing them to work together in ways they haven't before.
A group of rogue ninja who are hunting nekoshou for their special powers could be the main antagonists. They see Naruto's newfound connection with the nekoshou as a threat and try to eliminate him and the nekoshou he is protecting.