The main villain could be a powerful and ancient magical being that was previously unknown in the regular Harry Potter universe. This being might have awakened in the alternate dimension due to some magical accident. It wants to reshape the wizarding world according to its own twisted vision, and Harry and his friends must stop it before it's too late.
In the alternate dimension, Sirius Black could have turned out to be the main villain. He might have joined Voldemort from the start, using his skills and knowledge of the wizarding world to help the Dark Lord. He could be leading a group of Death Eaters in a new and more dangerous plot against the remaining resistance in the wizarding world.
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.
In an alternate dimension fanfiction, Neville Longbottom could take center stage. He could be the hero who rises up against the dark forces. Luna Lovegood might also be a main character, with her unique perspective on the alternate wizarding world. And we could also have new characters that are exclusive to this alternate dimension. For example, a Muggle - born wizard who has the power to control time, and he teams up with Harry and his friends to save the wizarding world from a new threat that emerged in this alternate reality.
One idea could be that in the alternate dimension, Voldemort won the war long ago. Hogwarts is now a dark and dreary place, with Death Eaters as teachers. Harry and his friends, who are part of an underground resistance, have to find a way to travel back in time to change the course of history.
A possible main villain could be an ancient sorcerer from the new dimension who has been awakened from a long slumber. He's enraged that the wizarding world has been interfering with his dimension's magic, and decides to take revenge on Harry Potter's world. He has powers that are unknown to the normal wizarding world, like the ability to control time in his dimension, which makes him a formidable foe.
One idea could be that in the alternate dimension, Voldemort won the war and Hogwarts is now a dark and dreary place where students are taught only dark magic. Another could be that the wizarding world is merged with the Muggle world in a strange way, like there are magical creatures running amok in London streets. Or perhaps in this alternate dimension, Harry was sorted into Slytherin and has to deal with a whole different set of challenges and prejudices.
In an alternate dimension, the main antagonist could be a dark entity that has emerged from the very fabric of the dementions themselves. This entity could be using the Dementors as its minions, controlling them to do its bidding. It would be a powerful and mysterious foe, and Harry would have to discover its true nature and weaknesses in order to defeat it.
A Hufflepuff prefect could be the main character. They are responsible for maintaining order within the house and could be caught in the middle of a power struggle between the different houses in this alternate universe. They would have to use their Hufflepuff traits to resolve conflicts and keep the peace in Hogwarts.
Hermione is also a popular character in these fanfics. Many alternate endings might show her in different relationships, not just with Ron. Maybe she could have a more independent life, traveling the world to study different forms of magic and using her intelligence to solve global wizarding problems.
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.
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 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.