A good choice for the main villain could be a Death Eater in disguise. They could be posing as a new teacher or a staff member at Hogwarts. Their goal could be to find out more about Harry Potter and try to weaken him before Voldemort fully returns. They could be secretly spreading dark magic and influencing some of the students to do their bidding. This would create a lot of mystery and danger within the Hogwarts walls. Since it's the third year, Harry and his friends would have to be extra vigilant as they are still young and inexperienced compared to later years.
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.
Perhaps a powerful magical creature that has been corrupted by dark magic could be the main villain. This creature, like a Hippogriff that has been enchanted wrongly, could be causing chaos around Hogwarts. It could be attacking students and teachers, and Harry and his friends would have to figure out how to break the dark magic spell on it. They would have to study old spells and potions, and maybe even seek help from some of the more knowledgeable professors like Dumbledore or McGonagall.
It could also be a dark wizard from the past who has been trapped in a hidden part of Hogwarts and is now released during Harry's third year. This wizard could have a vendetta against the Potter family or Gryffindor house and start causing trouble.
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.
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.
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.
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.
It could be a new student at Hogwarts. This student could have a unique background, like coming from a family of magical healers who have different views on magic compared to the traditional pure - blood families. Their fresh perspective could lead to the creation of the third path.
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.