It could be the White Walkers if this is a crossover fanfic set in the Game of Thrones universe. They are a huge threat to the Starks in their own world, and Harry Potter would have to find a way to stop them.
There might also be some rival houses or clans in the Stark's world who see the Starks as a threat to their own power. These could be the main antagonists, and Harry Potter would have to use his wits and magic to keep the Starks safe from their political machinations and possible attacks.
Well, perhaps he uses his magic skills. He could cast protective spells around the Starks' territory, like a powerful Fidelius Charm to keep their location secret from their enemies.
It could be a new dark wizard who wants to make a name for himself. He sees Hogsmeade as an easy target to show his power. He starts by causing small disruptions like making objects in the shops move on their own and then escalates to more dangerous attacks that Harry has to stop.
In many cases, the main antagonists can be other Slytherins who still hold grudges against Harry or are loyal to the pure - blood supremacist ideology. They might see Harry as a threat to their way of life. Also, some Death Eaters can be antagonists. They target Harry because of his role in Voldemort's downfall and would stop at nothing to get to him.
Another possible antagonist could be a power - hungry pure - blood family. They might see Harry as an impostor as the heir, believing that only a pure - blood should hold such a title. They would try to undermine Harry at every turn, spreading rumors and creating obstacles for him both in school and in the wizarding world.
New dark wizards or witches could emerge. They might target Harry's children, seeing them as a potential threat in the future due to their connection to Harry Potter. They could try to kidnap the children to use them as leverage against Harry or to turn them to the dark side.
Voldemort would still be a major antagonist. His quest for power and domination in the wizarding world would directly oppose the female Harry Potter, just as in the original series. His Death Eaters would also be a constant threat, causing chaos and harm.
It could be some of the pure - blood supremacists. They might see her as an abomination because of her connection to Hecate, who is not part of the traditional wizarding families. They would try to undermine her at every turn and make her life difficult at Hogwarts.
One possible main antagonist could be a dark wizard who is envious of Eros's powers or the relationship between Eros and Psyche. This dark wizard could be trying to disrupt their relationship and steal their magic for his own evil purposes. Maybe he was once rejected by a love, and seeing Eros and Psyche's love makes him want to destroy it.
Voldemort could still be the main antagonist. His goal of taking over the wizarding world wouldn't change just because of Harry's new heritage. In fact, he might see Harry as an even greater threat now that he has the potential of Yoruichi's powers. Another antagonist could be some of the pure - blood supremacists in the wizarding world who are afraid of the new kind of magic that Harry might bring in with his connection to Yoruichi.
The main antagonists could be a combination of forces. Besides Voldemort and his Death Eaters, there could be some anti - alien groups from the Muggle world who discover Harry's true identity. They fear his power and try to hunt him down. This would put Harry in a difficult position as he has to protect not only the wizarding world but also himself from these new threats that are coming at him from different directions.