It could be a Death Eater who has somehow made a pact with a powerful force from Scorpian's world. This villain would be extremely dangerous as they'd combine the dark magic of the Harry Potter universe with the unknown and potentially deadly powers from Scorpian's realm.
A group of dark wizards from both worlds could team up. Some Death Eaters from the Harry Potter side and some evil sorcerers from Scorpian's world. They form an alliance to find a powerful magical item that, when combined with a Scorpian - world artifact, would give them ultimate power over both universes. Their combined knowledge and resources would make them a formidable foe for the heroes in the fanfiction.
Maybe a corrupted wizard who has been studying Scorpian - world magic and technology in secret. He becomes power - hungry and decides to use this new knowledge to take over both the wizarding world and Scorpian's world. He starts by creating chaos at Hogwarts, using dark spells and strange devices that the students and teachers are not prepared to face.
Another option could be a new character created specifically for this crossover. This character could be a wizard who has studied the ninja arts and has become corrupted by power. He could start by causing chaos in the wizarding world, using his magic to mimic some of the more dangerous ninja techniques. Then, he could set his sights on the ninja world, seeing it as another source of power to be conquered. Fem Naruto and Harry Potter would have to put aside their differences and work together to stop him.
It could be a wizard who has gone mad with power and wants to control both the wizarding world and the underwater realm. He discovers a way to use dark magic to manipulate sea creatures and cause destruction in Aquaman's kingdom. He then sets his sights on Hogwarts as well, seeing it as another source of power.
Voldemort could still be the main villain in a different way. Suppose he discovers Tonks' unique connection to Harry and tries to use her as a weapon against him. He could manipulate her mind or put her in dangerous situations to force Harry to make sacrifices or bad decisions.
In a Harry Potter Scorpian crossover, Scorpian could be a new student at Hogwarts. He'd bring his unique skills and knowledge from his own world. For example, he might be an expert in some form of combat that the Hogwarts students have never seen before. He could then form an unlikely friendship with a group of Gryffindors, and together they face a new threat that combines elements from both their worlds, like a dark wizard using Scorpian - world technology to gain power.
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.
Lex Luthor from Supergirl's world could be the villain. He could somehow find a way to travel to the wizarding world and team up with some dark wizards. He wants to use magic to enhance his power and take over both worlds. Supergirl and Harry Potter would have to stop his evil plans.
It could be a new character created by the fanfiction author. Maybe a powerful wizard who was once shunned by the wizarding community and now wants revenge by stealing magic.
A dark wizard who has merged the dark arts with Wonderland's magic could be the main villain. He might have created some sort of dark Wonderland where all the creatures are under his control, and Harry has to break this control to restore balance.
A possible main villain could be a dark wizard who has learned some of the criminal tactics from the Detective Conan world. He could be using both magic and devious non - magical schemes to cause chaos. For instance, he might use spells to steal valuable items and then use the underworld connections in Conan's world to sell them.
Maybe the main villain could be a corrupted Hogwarts professor. This professor could be secretly teaching dark magic to students and when Harry's child discovers this, they become the target. The professor wants to stop the child from revealing their dark secrets and will go to great lengths to do so, making them a formidable villain in the fanfiction.