The Spirit of the Millennium Items could also be the main antagonist. They were initially in harmony with Atem, but with his turn to evil, they might try to resist his control. Since they are powerful entities in their own right, they could become a force against Atem. They would not want to be used for evil purposes and would fight back against Atem's newfound malevolence.
One possible plot could be that Atem is influenced by a dark magic artifact. Maybe he stumbles upon an ancient relic during an excavation in the afterlife. The relic starts to corrupt his thoughts, making him believe that only through domination can there be true order in the world. So he begins to use his powers to subdue the spirits around him.
The main antagonist could also be a new character created specifically for the fanfic. This character could be an ancient evil that has been waiting for an opportunity to corrupt a powerful Huntress like Ruby. They would then use Ruby's newfound evil nature to further their own dark plans, and Weiss, Blake, and Yang would have to face both Ruby and this new threat.
Another possibility is that Twilight herself could be the main antagonist in her own internal struggle. As she turns evil, there could be a part of her that still resists this change deep down. So, the evil side of Twilight that is taking over could be seen as the antagonist to the good side of her that is fighting to regain control.
It could be HIM. Since he has always been a major villain in the Powerpuff Girls universe, he might find a new way to turn the girls evil in this fanfiction. Maybe he uses a more insidious form of his magic this time.
It could be Yuno. Normally they are friends, but if Asta turns evil, Yuno might be the one to oppose him. Yuno has his own strong magic and a sense of justice that would make him a natural adversary.
Obviously, the evil Naruto himself would be the main antagonist. He's the one causing trouble in the Teen Titans' world, so he takes on that role.
Gary could be the main antagonist. He has always been Ash's rival and seeing Ash turn evil, he might feel responsible to stop him. Gary could gather his own team of powerful Pokémon and use his wits to oppose Ash at every turn.
The Guys in White could be the main antagonists. If Danny becomes evil, they might see this as their chance to finally capture and experiment on him. They would be constantly chasing him, which would make Danny see them as the main obstacle in his new evil plans, and thus they would be the antagonists in the story.
The obvious choice could be the creator of the evil doll. Maybe it's a rogue Death Eater who has found a new and unique way to cause trouble at Hogwarts. They use the doll as their proxy to spread fear and chaos without being directly detected.
Dumbledore could be the main antagonist. Harry might see Dumbledore as having used him all along for some grand plan. If Harry turns evil, he would want to break free from Dumbledore's influence. Dumbledore, with his power and wisdom, would then try to stop Harry from causing too much harm, thus becoming the main opposing force.