Maybe an unknown entity from another dimension. This being could be interested in using X Sans as a tool to invade or disrupt his world. So, it brainwashes him to make him do its bidding without resistance.
It could be a rival from X Sans' past. Someone who has always been jealous of X Sans' power or popularity in the fanfic world. This character might have finally found a way to get revenge by brainwashing him.
Well, it could be about an evil force taking over X Sans' mind. Maybe some powerful magic or a new villain in the fanfic universe. This brainwashing might lead him to do things that are against his normal nature, like fighting his friends or causing chaos in his world.
Another possibility is that it could be an alternate version of one of Cross's friends. This alternate version has been corrupted in some way and wants to drag Cross down with them. They use their knowledge of Cross's weaknesses and insecurities to successfully brainwash him, believing that they are doing the right thing or that they are actually helping Cross in some warped way.
Well, it could be that Cross is exposed to some sort of mind - controlling device or magic. Maybe an enemy uses a special spell to make Cross forget his true loyalties and start working for them. For example, the enemy could make Cross believe that his former friends are actually his foes and he has to fight against them.
There could be an ancient evil spirit that has a vendetta against griffins. When it senses that Cousland has befriended a griffin, it targets them both, trying to destroy their new - found bond and cause chaos in the world they inhabit.
It could be a powerful AI or a mad scientist. They might see Casshan's power and want to control him by brainwashing, so they would be the antagonists.
The most obvious antagonist would be the Millennium Earl. He has the motive and the means to brainwash Allen. He wants to destroy the Black Order and Allen, with his Innocence, is a major threat to the Earl's plans. So, by brainwashing him, he can turn that threat into an advantage.
A dark entity from another dimension could be the main antagonist. It senses Anna's new powers and wants to use them to open a portal between dimensions so that it can bring its army of monsters into Anna's world. So it constantly hunts Anna down, trying to either force her to use her powers for its own evil plan or simply kill her and take the powers for itself.
A jealous carnival owner could be the antagonist. He doesn't like Beppi teaming up with Djimmi because he fears their combined popularity will overshadow his own carnival. So he tries to sabotage their shows and separate them.
It could be a rogue ninja who has a grudge against their village. This ninja might target Chocho and Karui because they are seen as rising stars in the village. The rogue ninja could try to disrupt their training or missions, causing trouble for them and testing their friendship.
A jealous gamer who doesn't like the idea of Vanellope and Hiro teaming up could be the antagonist. This person might try to hack into the systems that connect their two worlds and cause chaos.