It could be the Death Eaters who see Harry's new - found mastery of darkness as a threat to their own power and ideology. They might try to either recruit him or destroy him. Voldemort himself could be an antagonist, feeling that Harry is encroaching on his territory as the most powerful dark wizard.
There could be an ancient dark wizard or a powerful dark entity that has been awakened by Harry's exploration of the dark arts. This entity might want to use Harry for its own evil purposes or simply destroy him because he represents a potential rival in the world of darkness. The Ministry of Magic could also be an antagonist if they see Harry's dabbling in the dark arts as a danger and try to arrest or contain him.
There could be a powerful dark entity that has been awakened by Harry Potter's newfound mastery of fire and darkness. This entity could be an ancient evil that was once sealed away and now wants to use Harry for its own dark purposes or simply destroy him as he is a potential obstacle.
The pure - blood supremacists could be the main antagonists. They might oppose Harry's ideas of a more inclusive and democratic political system as they believe in the superiority of pure - blood wizards.
Obviously, Voldemort could still be the main antagonist. He would be intrigued and threatened by Harry's new power, the lightsaber. Also, some Death Eaters might team up with dark wizards from other lands who are also after the power of the lightsaber.
The Ministry of Magic could be antagonists. If they start to oppress those with different views, including Harry, it could drive him towards darkness. Their corrupt and unjust actions might make Harry think that the only way to fight back is by using dark magic.
The Ministry of Magic could also be antagonists. They are often very strict about magic use and might not approve of Harry's exploration of wandless magic. They could try to stop him, fearing that it would disrupt the established order of magic that is mostly wand - based. The Ministry officials might see Harry as a troublemaker and try to put him under surveillance or even arrest him if they think he's getting too powerful in wandless magic.
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.
The plot might center around Harry being the master of darkness as a way to subvert the prophecy. Instead of being the 'Chosen One' in the typical light - against - dark way, he uses the knowledge of the dark arts to understand and outwit Voldemort. He could be learning long - forgotten spells from the darkest corners of Hogwarts library and using them to his advantage.
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.