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.
The main villain could be a sentient magical force in the new dimension. It was born out of the chaos and magic that was misused in the past. This force views all living wizards as a threat to the new dimension's stability. It targets Harry because he is seen as a symbol of the old wizarding ways. It has the ability to possess other wizards and use their powers against Harry and his friends.
It might be a corrupted version of Dumbledore from the new dimension. In this dimension, something went horribly wrong and Dumbledore turned to the dark side. He wants to use his knowledge of both dimensions to rule over all of magic. He manipulates events and people in the new dimension and tries to draw Harry into his web of lies and dark magic.
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.
Perhaps a group of rogue time - traveling wizards. They come from a future in this dimension where the wizarding world has been destroyed, and they believe that changing the past (even if it means causing chaos) is the only way to save their future. They see Harry as a threat to their plans because he has a natural inclination to preserve the present order.
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.
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.
It could be a long - lost relative of Voldemort, carrying on his dark legacy.
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.
One possible interesting plot could be Harry finding a new magical dimension where the rules of magic are completely different. For example, instead of using wands, magic is controlled by thoughts alone. He has to learn these new ways quickly to face a dark threat that exists in this dimension which is planning to invade the wizarding world he knows.
Perhaps the main villain is actually a corrupted version of a well - known character. For example, if Hermione was somehow influenced by the dark magic associated with the runestone path and turned against Harry. It would be a very unexpected and heart - wrenching twist, as she has always been such a loyal friend. But the power of the runestone path could be so strong that it changes her fundamental nature.
Maybe a new character, a Muggle - born wizard who was shunned by both the Muggle and wizarding worlds. This character, out of bitterness, decides to combine Muggle technology and magic to create the droid army and rule over both worlds. He would see Harry Potter and his friends as the main obstacles to his grand plan.