Who could be the main villain in a Harry Potter third year fanfic?
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.