Another possibility is that an overzealous member of the Order who has gone too far in their methods of fighting Voldemort. Their extreme actions might make Harry think they have become as bad as the Death Eaters, so he starts to oppose them. For example, if this member starts using unethical spells on innocent people in the name of the greater good.
It could also be an outside force, like a powerful dark wizard who is not directly associated with Voldemort but has his own agenda. This wizard might see the Order as a threat to his plans and uses Harry's trust in him to turn Harry against the Order. He could be providing Harry with false justifications and promises to make Harry believe that fighting the Order is the right thing to do.
There could be a group of rogue witches and wizards who are against the current system in the wizarding world. They oppose the Ministry of Magic's rules and see Harry Potter as a symbol of the establishment they want to overthrow, so they become the antagonists.
Perhaps there's a plot where Harry has a vision of a future where the Order causes great harm. This vision is planted by an enemy of the Order. As a result, Harry decides to take pre - emptive action against the Order. He gathers his own group of allies who believe in his cause and they engage in a series of battles against the Order, with many twists and turns as the truth slowly unfolds.
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's hard to say without more details about the fanfiction. But it could be some characters who benefit from Teddy not having rights, like power - hungry individuals or those with prejudiced views.
It could be a group of dark wizards who have a different ideology from Voldemort. They might not be interested in pure - blood supremacy but rather in power for power's sake. They could be more cunning and use more psychological warfare against Harry, which would force him to fight in new ways.
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.