An ancient evil sorcerer who has been awakened and senses the power within Merlin's sister. This sorcerer wants to use her power for his own dark purposes and will stop at nothing to capture her and bend her to his will. He could send his minions after her and create all sorts of obstacles for her throughout the fanfiction.
Agravaine could also be a main antagonist. He could suspect that Merlin's sister is involved in Merlin's activities against him and King Arthur. He would then try to find a way to use her to get to Merlin or to simply get rid of her as a potential problem.
Morgana could be a great antagonist. She might see Merlin's sister as a threat to her own plans for Camelot. Maybe she discovers that Merlin's sister has a power that could undermine her magic or her influence over the court.
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.
Perhaps a powerful and corrupted spirit that guards Merlin's Castle and sees Harry and his friends as intruders. This spirit might have its own evil agenda and try to stop Harry from achieving whatever goal he has in the castle, like obtaining a powerful artifact or knowledge. It could use all sorts of dark magic and illusions to deceive and harm them.
It could be Morgana. Since she was always at odds with Merlin and Camelot, his death wouldn't stop her from her plans. In fact, she might be emboldened by it. She could use the chaos that follows Merlin's death to her advantage, trying to take over Camelot more easily. Also, there could be some dark magic force that was previously held at bay by Merlin. Now that he's gone, this force could become the main antagonist. It could be something like an ancient evil that Merlin was constantly keeping in check, and without him, it starts to spread and cause destruction.
Maybe an anti - elf group within Camelot. They see the elven apprentice as a threat to the kingdom and will do anything to get rid of the apprentice. They could be led by a noble who has a deep - seated hatred for the elves and views the relationship between Merlin and the apprentice as a danger to Camelot's stability.
Morgana could be the main antagonist. She might see Merlin's transformation as an opportunity to further her own plans. Since Merlin is in a more vulnerable state as a girl, Morgana could try to use this to her advantage, perhaps by trying to turn the court against Merlin or using her new form to manipulate her into doing things that would harm Camelot.
It could be a rogue Death Eater who survived Voldemort's fall and blames Harry and his sister for the downfall of their cause. This Death Eater might be more cunning and powerful than the others, and he targets Harry's sister specifically because she represents a new threat to their dark plans. He might try to use her as a pawn to draw Harry out and then destroy them both.
It could be an ancient monster that has a grudge against the family of Poseidon. Since Percy and his twin are children of Poseidon, this monster might target them specifically. Maybe it's a sea serpent that was once defeated by Poseidon and now wants revenge by going after his descendants.