It could be a corrupted Ministry of Magic official. This official wants to use the Muggle world for his own gain, and he sees Kate Beckett as a threat. He teams up with some dark wizards and tries to stop Harry and Kate from uncovering his plans. This would create a complex web of intrigue as Harry and Kate have to fight against not only dark magic but also the corruption within the wizarding world.
It could be a criminal mastermind who has a vendetta against Beckett or someone close to her. This antagonist might see the baby as a way to get back at Beckett, either by using the baby as bait or harming it to cause her pain.
Perhaps a long - lost relative of the Potter family who feels they were unjustly excluded from inheriting the manor. This relative could be jealous of Harry's status and the wealth associated with the manor. They might use dark magic to try and claim what they think is rightfully theirs, leading to a battle of magic and loyalty within the Potter family and among Harry's friends.
One idea could be a crossover where Kate Beckett, with her detective skills, is transported to the wizarding world of Harry Potter. She could help solve a mystery that has stumped the Ministry of Magic. Maybe it's a case of a dark wizard using Muggle - like technology in a devious way, and her knowledge of modern forensics combined with the magic of the wizarding world would make for an exciting story.
A new dark wizard or witch could be created specifically for this fanfiction. This character could be interested in using the Huntsman's skills for their own evil purposes. If the Huntsman refuses, they become enemies. This antagonist could have powers related to dark forest magic, something that the Huntsman is familiar with but in a more malevolent form.
Voldemort could still be the main antagonist. Even if Demetri has some sort of connection or change in the fanfiction, Voldemort's overarching evil plans would still be a major threat to both Harry and Demetri, especially if Demetri tries to deviate from the Death Eaters' path.
The minotaur itself could be the main antagonist. It's a powerful and dangerous creature, and if it's been set loose in Hogwarts or is guarding something that Harry needs, it would be a major obstacle for him to overcome.
The main antagonist could be a dark wizard who has made the graveyard his lair. He uses the dark energy from the tombstones and the restless spirits there to power his dark magic. Harry stumbles upon this wizard's activities and has to stop him.
A new dark wizard or witch could be the main antagonist. This character, jealous of Harry's fame and power, creates a situation where Harry is framed for a heinous crime. They then ensure his arrest so that they can take over the role of the 'chosen one' in the eyes of the wizarding public and start spreading their own brand of dark magic.
It could be Malfoy. He might make fun of Harry for wearing a dress and try to use it to humiliate him in front of the whole school, which would then lead to a conflict between them that goes beyond the usual rivalry.
Perhaps a new dark wizard or witch who has infiltrated the Ministry of Magic and made sure Harry was sent to Azkaban. This antagonist could be working towards a bigger plan to take over the wizarding world and sees Harry as a major threat even when he's locked up.