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.
One possible plot could be that Thor somehow gets transported to the wizarding world. He might initially be confused by the magic there as it's different from his Asgardian powers. Harry Potter and his friends could be intrigued by Thor and his hammer. They might team up to fight a common enemy, perhaps a dark wizard who has somehow got hold of some Asgardian artifact and is misusing its power.
It could be Loki. Since he has a knack for causing trouble, he might find a way to cross over to the wizarding world. He could manipulate the dark wizards and use their magic for his own devious plans. Maybe he wants to steal the Philosopher's Stone to gain immortality and use it to take over Asgard as well.
One possible plot could be that Thor ends up in the wizarding world of Harry Potter. Maybe the Bifrost malfunctions and he lands near Hogwarts. He could be mistaken for a very powerful wizard at first. Then he teams up with Harry Potter and his friends to fight against a new dark threat that is using both magic and some form of Asgardian - like power. Thor could teach the wizards about Asgardian combat and they could teach him more about the nuances of magic.
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.
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.
Loki could be a great main villain. He could be secretly fueling the Civil War for his own gain, like trying to take over Asgard while everyone is distracted. He has the cunning and the motivation to do so.
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.
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.