It could be Draco Malfoy. He might not like the idea of Harry getting a second chance at the OWLS and tries to sabotage him. Maybe he spreads rumors about Harry not being worthy of a retake.
The Ministry of Magic could be the antagonists. They might have strict rules against retaking OWLS and try to stop Harry. They could be worried that if Harry is allowed to retake them, other students will demand the same. So they send officials to make things difficult for Harry during his retake.
Well, maybe Harry discovers he didn't do as well as he hoped on his OWLS the first time. So he decides to retake them. He might study new spells and magical theories that he missed before. He could also face some challenges from other students who don't like the idea of him getting a second chance.
Voldemort's remaining followers could be antagonists. They might target Harry's little sister thinking they can use her to get to Harry. They could try to kidnap her or use dark magic on her.
There could be some old - fashioned professors at Hogwarts who are against Harry's unorthodox ways of making his mark. They believe in the old - established ways of teaching and practicing magic and see Harry as a troublemaker who is disrupting the order of things at the school.
It could be a group of dark wizards who are jealous of Harry's status and see Lemon as a way to get to him. They might try to kidnap her or manipulate her to get Harry to do their bidding.
One possible antagonist could be a corrupt wizard in a high - ranking position in the Ministry of Magic's financial department. This wizard might be trying to cover up his misdeeds and would see Harry as a threat to his scheme.
The Thalmor could be great antagonists. Their strict control over magic and their anti - human beliefs could put them at odds with Harry. They might see his different form of magic as a threat to their power in Skyrim.
Scarecrow could also be a main antagonist. His fear - inducing toxins could be a real problem for Harry. Harry would have to use his magic to counter the effects of the fear toxin and also figure out a way to stop Scarecrow from spreading it all over Gotham.
Voldemort could still be the main antagonist. He might see Harry's connection to the monsters as a threat to his own power and try to either use it for himself or destroy Harry to prevent him from uniting the monsters against him.
There could also be a trainer who is jealous of Harry's unique abilities, being reborn from the Harry Potter world. This trainer might try to undermine Harry at every turn, stealing his Pokemon or sabotaging his battles, much like Draco Malfoy was often in conflict with Harry in the original Harry Potter series.
There could also be some characters from the Doctor's universe who oppose the idea of a half - wizard, half - Time Lord. They might come to the wizarding world to try and stop Harry from using his combined powers, fearing it could disrupt the balance between the two universes.