The main antagonists could be the scientists or the people in charge of the Weapon X program. They would see Harry as an experiment or a threat to their plans.
In this fanfiction, the main antagonists could be the directors of the Weapon X program. They are likely to be cold - hearted individuals who care only about the success of their program. They would see Harry as a valuable asset, and when he tries to escape, they would send their most elite guards, who might be mutants or highly - trained soldiers, to stop him. Harry would have to use his wits and magic to get past these antagonists.
In such a fanfiction, perhaps Harry Potter uses his magic skills, like the Patronus charm, to fend off the threats in the Weapon X program. He might also use his intelligence to outwit the people running the program.
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.
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.
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.
It could be a powerful dark wizard who has a grudge against the goblins and wants to destroy Gringotts. This wizard might have been wronged by the goblins in the past, and now he's seeking revenge by trying to bring down the bank. He could be using his own army of dark creatures to attack Gringotts.
The Death Eaters would be obvious antagonists as they are in the original Harry Potter series. But also, there could be a group of shadowy figures from Nightwing's world who oppose the idea of a wizard - Nightwing hybrid. They see Harry as an abomination and try to eliminate him before he can fully realize his powers.