Sometimes, corrupt members of the Ministry of Magic can be the main antagonists. They may oppose Harry's attempts to seek justice because it threatens their power and the status quo they've maintained for so long.
It could be the remnants of the Death Eaters. Even after Voldemort's fall, some of them might still be causing trouble and Harry Potter has to bring them to justice for their past and present crimes.
In certain fanfictions, a new dark wizard or a group of dark wizards could emerge as the main antagonists. They might be causing chaos and harm, and Harry Potter is determined to seek justice against them to protect the wizarding world.
The Death Eaters are often common antagonists. Since they were the main followers of Voldemort, and Harry has every reason to be vengeful towards them for all the harm they caused. They killed many innocent people and were a constant threat to the wizarding world.
In some fanfictions, Harry Potter seeks justice for the wrongs done to the house - elves. He could fight against the discriminatory treatment they face in the wizarding world, perhaps by introducing new laws or creating a sanctuary for them.
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.
Another possibility is that there could be a magical creature that has some sort of grudge against Fawkes. This creature might see Harry as an obstacle because of his bond with Fawkes. It could be an ancient and powerful creature that has its own motives and goals that conflict with Harry and Fawkes' relationship.
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.
Voldemort or his followers might also be antagonists. Even if Voldemort is defeated in the original story, in this fanfiction, his remaining Death Eaters could see Harry's new power as something they can either use or must destroy. Or perhaps a new dark wizard inspired by Voldemort's ideology rises up against Harry.
It's hard to say for sure without reading the fanfiction. But it could be the usual suspects like Voldemort and his Death Eaters. However, with Kratos in the picture, there might be new antagonists from Kratos' world who see Harry as a threat now that he's being trained by such a powerful being.
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 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.