One potential antagonist could be an ancient magical entity that has been awakened by the experiments of the Unspeakables. It sees Harry and the Unspeakables as a threat to its existence and tries to destroy them. Additionally, there could be a group of anti - Ministry wizards who believe that the Unspeakables are dabbling in dangerous magic and they target Harry as a symbol of the Unspeakables' activities.
In this fanfiction, Harry could be brought into the Unspeakables to deal with some ancient and powerful magic that has been awakened. He may start off as an outsider among the Unspeakables, but gradually earn their respect. His adventures within the Department of Mysteries could include uncovering long - lost spells and artifacts. This could also lead to a conflict between his loyalty to his old friends and his new responsibilities within the Unspeakables.
Obviously, Voldemort could be one of the main antagonists. He might be the one who lures Harry into the League of Doom in the first place, with false promises. Another could be Bellatrix Lestrange. She is extremely loyal to Voldemort and would be very suspicious of Harry's presence in the league and try to expose or kill him.
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.
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.
There could be a group of anti - military rebels outside the military. They see the military as a tool of oppression and are constantly causing trouble. Percy might have to deal with them, either through combat or trying to negotiate and understand their point of view.
Voldemort would likely be the main antagonist still. He might see Harry's potential as an animagus as a way to strengthen his own forces. His Death Eaters would also play a role in trying to convince Harry to join the dark side.
It could be the other Titans who don't want a half - wizard, half - Titan like Harry to exist. They might see him as a threat to their pure Titan bloodlines or their power structure.
The Death Eaters could still be the main antagonists. They might see Fenrir's new alliance with Harry as a threat. Since they once used Fenrir for their dark deeds, they don't want him to turn good and expose their secrets.
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.