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.
Maybe Harry discovers a new and unique magic that only he can perform. This new magic could be the mark he makes. For example, he might find a way to combine different spells in an unprecedented way that gives him an edge in fighting the dark forces.
Some of the die - hard Death Eaters could also be antagonists. They might not trust Harry even with the Dark Mark and try to undermine him or expose his true intentions if they suspect he's not truly on their side. Bellatrix Lestrange, for example, is so fanatical about Voldemort that she would be a likely candidate to oppose Harry even if he seems to be part of the 'dark' group.
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.
Hermione could be there. She would be really helpful in planning and organizing the island. For example, she might set up a system for categorizing all the magical knowledge and resources on the island.
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.
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.
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.
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.
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.
Maybe Malfoy could be an antagonist. He might be jealous of Harry's new project and try to sabotage it, thinking that Harry is getting more attention again.