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.
One antagonist could be a rogue wizard who has made a pact with some dark forces from Nightwing's realm. This wizard wants to take over both the wizarding world and the world related to Nightwing. He sees Harry as the biggest obstacle because of his combined powers. Also, some of the more traditional pure - blood supremacist families in the wizarding world might oppose Harry because of his non - wizard heritage on his father's side, seeing it as a threat to their idea of a pure magical bloodline.
There could also be some characters from the Doctor's universe who oppose the idea of a half - wizard, half - Time Lord. They might come to the wizarding world to try and stop Harry from using his combined powers, fearing it could disrupt the balance between the two universes.
It could be some dark wizards who are threatened by Harry's unique heritage. They might see him as a potential threat to their power and plans. Maybe they want to use his connection to Spike for their own evil purposes and when Harry refuses, they become his enemies.
The main antagonists could still be the Death Eaters. Since they are the traditional enemies in the Harry Potter universe. They would see Harry, even as the son of Ziva David, as a threat to their dark plans. They might target him not only because of his connection to Harry Potter but also because they fear the unknown elements that Ziva's heritage could bring into the fight against them.
Voldemort could still be a main antagonist. His dark magic and thirst for power would put him at odds with Harry, especially if he sees Harry's connection to Black Widow as a threat. Another could be some of the more traditionalist wizards who don't trust Harry because of his strange heritage.
The Death Eaters could still be the main antagonists. Even though Harry has this new connection to Lady Magic, the Death Eaters, loyal to Voldemort, would see him as a major threat to their dark plans and would continue to try to kill him.
It could be another magical creature or group that is jealous of the power that the vixen holds and by extension, Harry as her adopted son. Maybe there is a group of dark wizards who want to harness the vixen's magic through Harry, and they become the antagonists as they try to capture him.
The Ministry of Magic could be the main antagonists. Since Harry is the abandoned son of Artemis, they might see him as a threat to the stability of the wizarding world. They could try to suppress his powers and keep his identity a secret.
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.
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.
One possible plot could be that Harry discovers his connection to Nightwing in a mysterious way. Maybe he starts having strange dreams or finds an old artifact that reveals the truth. Then he has to learn to balance his wizarding world life with this newfound heritage related to Nightwing, which could bring in new powers and a whole new set of challenges.