There is a possibility that an ancient and powerful dark creature could be the main villain. This creature, long forgotten in the wizarding world, resurfaces and targets Harry's son. It might believe that the boy has some special power or is the key to something it desires. As a result, it lures the son away and hides him in a remote and dangerous place. Harry has to figure out what this creature is and how to defeat it to get his son back.
Well, it could be about Harry's son getting lost in the wizarding world. Maybe he's exploring a new part of Hogwarts and gets trapped in a secret chamber. Or perhaps he's lured away by some dark magic users who want to use him against Harry.
Hermione would be a great main character. She's known for her intelligence and determination. She could be on a quest to find a lost book in the Hogwarts library that holds the key to solving a mystery, like a series of strange disappearances in the castle. Her knowledge of spells and research skills would be put to good use in the search.
It could be a rogue Death Eater who escaped punishment and has been biding his time. He might have a new, more insidious plan to bring back the dark ways of Voldemort.
The Slaughterhouse Nine could be the main villains. Their sadistic and unpredictable nature would pose a huge threat to Harry. Each member has their own unique and terrifying power. Harry would have to rely on his magical knowledge and any allies he can make in Brockton Bay to survive and stop the Nine from causing more chaos in the city.
It could be a descendant of Voldemort. Even though Voldemort was defeated in the original series, his ideas might have been passed down through generations. This new villain could be even more cunning and powerful, and they see Harry Potter, who has been frozen and is now back, as a threat to their plans of total wizarding world domination.
It could be a rogue wizard who was once a student at Hogwarts and has a vendetta against the school. He was expelled for practicing dark magic and now he's back to cause trouble. Maybe he wants to steal some powerful magical artifacts from the school's vaults.
A powerful dementor - like being that has been corrupted by Asgardian dark magic. This entity could be draining the life force of both wizards and Asgardians. It would be up to Thor and Harry Potter to find a way to stop it, as it poses a threat to both of their worlds.
It could be an alternate version of Dumbledore. Maybe in this dimension, he was corrupted by power. He uses his vast knowledge and influence to control the wizarding world for his own ends. He manipulates the students at Hogwarts and uses dark magic in secret while maintaining a public facade of being a great wizard.
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.
It could be a new dark wizard. Maybe a jealous former Hogwarts student who felt overshadowed by Dumbledore and now sees baby Harry and Hermione as threats to his future plans. He might want to use their power for himself or just eliminate them to make sure he can rise to power unopposed.