The Malfoys could be the main villains. They might have turned to even darker magic after the fall of Voldemort and formed their own secret organization. Lucius Malfoy could be using his wealth and influence to gather dark wizards and witches to create chaos in the wizarding world.
A new dark wizard, not related to Voldemort, could emerge. This wizard could be from a far - flung part of the wizarding world and have access to unique and dangerous magic. He could be recruiting followers and causing destruction, and Harry as a special agent has to figure out his motives and stop him.
The Death Eaters could also be major villains. They might team up with some anti - SHIELD groups in the muggle world. The Death Eaters' dark magic combined with the muggle - world weaponry of these groups could pose a serious threat to both the wizarding and muggle worlds that Harry and SHIELD have to stop.
There could be new villains like an evil wizard - scientist who wants to use magic to create black holes and destroy planets for his own gain. Or perhaps an alien race that has a natural ability to drain magic from wizards and witches and they see the Hogwarts students as a source of power.
It could be Death Eaters who have a new plan. They might want to create chaos in the Muggle world by targeting the Queen. They see her as a symbol of Muggle power and order, so by attacking her, they hope to disrupt the Muggle - wizard relationship.
One possible main villain could be an Egyptian wizard who has been corrupted by dark magic. He might be after some powerful Egyptian artifact that can give him ultimate power. He could see Harry as a threat to his plans because Harry has knowledge of different kinds of magic from Hogwarts.
The Akatsuki could still be the main villains. In a secret agent Naruto fanfic, they could be even more devious, using undercover agents of their own to disrupt the shinobi world while Naruto tries to stop their grand plan of collecting all the tailed beasts.
It could be a group of rogue Death Eaters who have formed their own empire after Voldemort's fall. They might be more radical and have new, even darker plans for the wizarding world.
It could be some of the remaining Death Eaters. They might target Amelia Bones because she is a powerful and important figure in the Ministry of Magic. Her knowledge and influence could be a threat to their plans of resurrecting Voldemort's ideology or causing more chaos in the wizarding world.
It could be a new student at Hogwarts. This student comes from a family that has a long - hidden knowledge about the special magical forces. They enter Hogwarts and start to share this knowledge with their new friends, causing a stir in the school. Neville could also be a main character. He has grown so much throughout the series, and he could use his newfound confidence to explore these special magical forces and prove himself even more.
It could be some Death Eaters who have made a deal with a Wakandan traitor. They might want to steal Wakanda's vibranium to make powerful dark magic items. The Death Eaters' dark magic would pose a serious threat to Wakanda's peace and stability.
There could be alien dark wizards. They might have their own brand of magic that is different from what Harry is used to on Earth. They could be trying to steal Earth's magic for their own evil purposes.