There could be a group of dark wizards who are working together to bring chaos to the wizarding world. They target Amelia Bones because of her position in the Ministry and Harry Potter because of his fame. This group, with their evil intentions and powerful dark magic, would serve as the main antagonists in the fanfiction.
A power - hungry wizard within the Ministry itself could be the antagonist. He sees Amelia Bones as a threat to his rise in power and also dislikes Harry for his influence among the wizarding community. He spreads false rumors about them and tries to get them in trouble, all while trying to further his own political agenda.
Perhaps a new dark wizard or witch who is jealous of Amelia Bones' power and influence in the Ministry. They might see Harry as a way to get to Bones, by either using him as a pawn or by trying to turn him against her. This new antagonist could have a unique and dangerous brand of dark magic that challenges both Harry and Amelia.
It could be a dark wizard who has infiltrated the Ministry of Magic. This antagonist might be trying to undermine Amelia Bones' work and also target Harry for his fame and power.
They could have a mentor - mentee relationship. Amelia, being older and more experienced, could guide Harry in his fight against the dark side.
Well, it could be about Harry Potter seeking Amelia Bones' help in solving a mystery within the wizarding world. Maybe a new dark magic threat has emerged, and Amelia Bones, with her expertise in the Ministry of Magic's law enforcement, teams up with Harry to get to the bottom of it.
It could be a power - hungry alien leader who wants to take over Hogwarts and use its magic for their own empire.
A dark wizard from the Harry Potter universe could be the main antagonist. Maybe a follower of Voldemort who escaped the final battle and found his way to Byakko's world. He sees the power of Byakko and wants to use it for his own evil purposes. He could try to enslave Byakko and use its power to take over both the wizarding world and Byakko's realm.
Most likely, Medusa would be the main antagonist. Her ability to turn people to stone makes her a very dangerous foe for Harry Potter and the other characters in the wizarding world.
It could be a dark fairy who wants to use the power of both the wizarding world and Pixie Hollow for her own evil purposes. She might try to steal the magic from Hogwarts and the pixie dust from Pixie Hollow to become all - powerful.
Maybe the main antagonist could be Ra's al Ghul. He's always interested in power, and if he got his hands on some magic from the Harry Potter universe, he could become an even greater threat. He could try to use the magic to bring about his vision of a 'perfect' world, which would be at odds with both Harry's and Nightwing's ideas of justice. So they'd have to join forces to stop him from achieving his goals.