There could be another mutant that was created earlier or as a result of the same incident that has turned evil. This other mutant could be jealous of the new mutant's relationship with Harry Potter or simply be on a path of destruction, and thus become the main antagonist in the story.
It could be a dark wizard who wants to use the mutant for his own evil plans. He might see the mutant as a powerful tool to gain control over the wizarding world.
Well, it could be a wild mix of magic and mutation. Maybe Harry Potter uses his magic to accidentally create a mutant in the world of 'sch' (whatever that is in the fanfiction context). It could lead to a whole new set of adventures as he tries to deal with the consequences of this creation, like trying to find a way to control or help the mutant.
Perhaps there's a member of the royal court who is secretly envious of Harry's power and tries to undermine him. This person could be plotting against Harry and trying to make the queen believe that he is a danger rather than an asset. They might spread false rumors or create false evidence to get rid of Harry.
It could be a new dark wizard who is jealous of Harry's ability to lift Excalibur. This wizard might want the sword for himself to gain ultimate power. He could start causing chaos in the wizarding world, trying to draw Harry out and take the sword from him. He might even team up with some of the Death Eaters who are also interested in the power the sword could bring.
Maybe the main antagonist is a dark force that has been slowly taking over the alliances from within. Harry notices this and decides to cancel the alliances to prevent the dark force from spreading further. This dark force could be something like an ancient evil that has awakened and is using the alliances as a way to gain a foothold in the wizarding world.
One possibility is that Harry Potter, using his knowledge of magic and experiences, decides to create a school for mutants. He could use spells to protect the school from the outside world and those who might fear the mutants. He might also teach the mutants how to control their powers, just as he learned to control his magic at Hogwarts.
This fanfiction could involve a whole new set of relationships. Harry, as a mutant in this concept, might find himself befriending mutants from the X - Men universe. He could learn from them how to control his new - found mutant powers while also teaching them about magic. There could be a conflict between the wizarding world that wants to keep magic separate and the mutants who might see magic as just another form of power. Also, the story could explore how Harry's mutant nature affects his standing in the wizarding world, whether he is accepted or feared.
It could be a new player on the team who is jealous of Harry's skills and popularity. This new player might spread lies about Harry, turning the other team members against him. So the new player would be the main antagonist in this scenario.
It could be a new dark wizard who has been secretly searching for the Death Stone. Maybe someone who was in the shadows during Voldemort's time and now sees an opportunity to rise with the power of this stone.
It could be a new dark wizard we haven't seen in the original series. Maybe someone who has a vendetta against Hogwarts and manipulates Harry into doing the dirty work of destruction.
Dumbledore could be seen as the main antagonist from Harry's new perspective on the dark side. Dumbledore represents all that is good in the wizarding world, and if Harry has turned to the dark, Dumbledore would be the one trying to stop him, to bring him back to the light. So in this context, Dumbledore becomes the opposition that Harry has to face.