The main antagonist could be an ancient evil spirit that has been awakened by the mixing of ninja and wizarding magic. This spirit is angry at the intrusion and starts to possess students and teachers at Hogwarts. The ninja and Harry Potter must figure out how to exorcise the spirit before it's too late and Hogwarts is completely taken over.
A dark wizard or witch from outside Hogwarts could be the main antagonist. They might target Harry specifically because of his reputation as the 'Chosen One' and use their influence to get him expelled from Hogwarts so that he is more vulnerable and easier to attack.
The main antagonist could be an old, corrupt house - elf. This house - elf was mistreated in the past at Hogwarts and has now turned to the dark side. It wants to bring chaos to Hogwarts and sees Lady Hogwarts as the key. It uses its knowledge of the school's hidden passages and secrets to plot against her. Harry Potter, being the defender of the underdog, tries to reason with the house - elf at first but when that fails, he has to use magic to stop it from harming Lady Hogwarts.
It could be a new dark wizard who is jealous of Harry's new mastery. This wizard might try to steal Harry's knowledge or use it for his own evil purposes. He could be a former Death Eater who was thought to be dead but has now returned with a vengeance.
It could be a new dark wizard who has been lurking in the shadows. Maybe someone who was once a student at Hogwarts but turned to the dark side.
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.
One possible plot could be a ninja from a far - off land arriving at Hogwarts under mysterious circumstances. Maybe they are on a quest to learn a special type of magic that only Hogwarts can offer. They could end up befriending Harry Potter and teaching him some ninja skills in return for learning about wizardry.
It could be a dark wizard who has infiltrated Hogwarts' staff. This wizard might be secretly manipulating events and students for his own dark purposes. He could be using his position to spread dark magic teachings and trying to turn students against each other, all while Lily Luna Potter starts to suspect something is wrong and tries to expose him.
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.
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.