It could be a dark magic user who doesn't want the human - turned - Twilight to succeed. Maybe this antagonist sees the new Twilight as a threat to their own power or plans in the pony world.
There could be an outside force, like an ancient evil that has been awakened. This force might target the human - turned - Twilight because they sense the new power and potential within them. It wants to corrupt the new Twilight or use their powers for its own dark purposes.
A jealous pony who was once close to Twilight could be the main antagonist. When the human becomes Twilight, this pony feels replaced and starts causing trouble. They might try to sabotage the human - turned - Twilight's attempts to fit in and use their powers for good.
Well, perhaps the human could be transported into the My Little Pony world and gradually take on the characteristics of Twilight. Maybe they start by learning magic like Twilight does, and as they do, they become more like her in personality too, like becoming more studious and dedicated to knowledge.
It could be another ghost who is jealous of Casper's new human form. This ghost might try to sabotage Casper's attempts to fit into the human world, perhaps by causing chaos around him and making humans afraid of him again.
It could be a vampire who resents Damon for becoming human. This vampire might see it as a betrayal of their kind. They could try to either turn Damon back into a vampire against his will or simply make his human life miserable.
The main antagonist could be a dragon hunter. Since Saphira is now in a human form and has lost her dragon defenses, the hunter sees her as an easy target. He might be after her because he believes that she has some connection to the dragons and he wants to use her to find the dragon lair or something valuable related to dragons.
A powerful witch could be the antagonist. She might have been the one who turned Damon human again against his will, and now she has some sinister plan for him. For example, she wants to use his new human form to perform some dark magic ritual that requires a human with a vampire past.
Her friends like Pinkie Pie, Rainbow Dash, Applejack, Rarity and Fluttershy are likely to be main characters. Pinkie Pie might bring her usual cheer and parties to celebrate Twilight's new form. Rainbow Dash could be both impressed and a bit competitive, trying to keep up with Twilight's new abilities in her own way. Applejack would offer her down - to - earth advice and support. Rarity might be excited to create new outfits for Twilight as an alicorn. And Fluttershy would be there with her gentle nature, providing a calming presence.
It could be a character who wants to use Percy - turned - Aku for their own evil purposes. Maybe a dark wizard who thinks that Aku - Percy can be the ultimate weapon to take over the world. This wizard would try to manipulate Percy's new form and powers to do his bidding.
Perhaps a powerful vampire lord who sees Sookie as a threat to his power. Since she was once human and has connections to both worlds, he might fear that she could rally other vampires and humans against him. He could try to eliminate her by any means necessary, leading to a lot of action - packed scenes in the fanfiction.
It could be Sasuke. If Sasuke has turned completely to the dark side and Naruto fails to save him, Naruto might be so frustrated and angry that it starts to make him cold - hearted towards everyone. Sasuke's actions could be the trigger for Naruto's transformation.
The Ministry of Magic could be the main antagonist. They might view Harry's fascination with Dementors as a sign of him turning to the dark side. So they try to stop him from his research and exploration of Dementors, fearing he'll use their powers for evil. After all, Dementors are associated with dark magic in the eyes of the Ministry.