Voldemort is the obvious main antagonist. But think about it, there could be a group of pure - blood supremacists who don't like Naruto because he doesn't fit into their idea of a proper wizard. He comes from a different world with different values. They could form an alliance with Voldemort or try to carry out their own malicious plans against Naruto and his friends at Hogwarts. Also, some of the Death Eaters who are still at large might target Naruto, seeing him as a new threat to their dark lord's plans.
Definitely Voldemort. However, there could also be some Slytherin students who are jealous of Naruto's power and popularity. They might try to undermine him and side with the Dark Lord. And in the background, there could be some dark creatures that Naruto has to face, like dementors or basilisks, which are influenced by the Dark Arts and Voldemort's presence.
It could be someone new, a dark wizard who has learned about Naruto's reincarnation and wants to use his power for evil. This new villain might try to manipulate Naruto into using his chakra in a wrong way. Or perhaps it could be a combination of Voldemort and some of Naruto's old enemies from his previous life who somehow find a way to merge their powers in the Harry Potter world.
One possible antagonist could be an Akatsuki member who has somehow gained knowledge of Naruto's Arthurian reincarnation and wants to use it for their own evil purposes. Maybe they want to steal the power that comes with it.
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.