The Joker could be a great main villain. He could infiltrate the school disguised as a new student or a janitor. He starts causing chaos by spreading his brand of insanity among the students, like setting up pranks that turn dangerous. Batman would immediately recognize his presence, but the Joker is always one step ahead in causing mayhem. Wonder Woman would have to use her lasso of truth to try and get information from the students who have been influenced by the Joker.
Cheetah could be a good main villain for this fanfiction. She could be a former student who was expelled from the school for her uncontrollable power. Now she returns with a vengeance, determined to destroy the school and everyone in it. She targets the weakest students first, using her speed and claws to create fear. Batman and Wonder Woman must find a way to stop her, either by trying to rehabilitate her or by force if necessary.
Lex Luthor could be the main villain. He could be funding the school secretly with an ulterior motive. Maybe he wants to create his own army of super - powered individuals. He manipulates the school's curriculum and resources to his advantage. Batman and Wonder Woman start to suspect something is wrong when students start showing unusual abilities that seem more harmful than helpful. They then have to expose Lex Luthor's plan and stop him before it's too late.
The Joker could also be a great choice as the main villain. He's always been obsessed with Batman. Now that Batman is getting married to Wonder Woman, the Joker could feel left out or enraged. He might try to ruin their big day in his own chaotic and unpredictable way. He could also target Wonder Woman as a way to get back at Batman, creating all sorts of mayhem in the process.
Lex Luthor could be a likely candidate. He is extremely intelligent and has a long - standing vendetta against superheroes. He might come up with a complex plan using his vast resources and scientific knowledge. For example, he could create a weapon that targets their unique abilities. He could also manipulate other villains and heroes alike to create a situation where Batman and Wonder Woman are isolated and vulnerable.
Lex Luthor could be a great main antagonist. He could be jealous of the trio's popularity and see them as a threat to his own power - hungry plans. He might create elaborate traps and use his vast resources and intellect to try and take them down, all while trying to make it look like they are the bad guys in the public eye.
Cheetah could be a great villain. She has a connection to Wonder Woman already, but in a crossover, she could be working with some of Batman's rogues like the Penguin. The Penguin could provide the resources while Cheetah does the dirty work in combat against Batman and Wonder Woman.
In this batman and wonder woman school fanfiction, the school could be a special academy for meta - humans. Batman and Wonder Woman are there to recruit the best students for a new superhero team. However, there is a rift between the students who idolize Batman's more brooding and stealthy approach and those who prefer Wonder Woman's open and powerful style. This causes conflicts within the school. But when an outside threat arrives, they all have to come together under the guidance of Batman and Wonder Woman to protect the school and prove that different styles can work together for a common good.
The Cheetah could also be a main antagonist. She could be working with some anti - hero or anti - superhuman group. She uses her speed and cunning to set up situations where Batman and Wonder Woman seem to be causing trouble. For example, she could steal something and make it look like they did it.
There could be an ancient evil that is awakened by the birth of their son. This entity could see the son as a threat to its plans for world domination. It might have powers that are beyond what the son initially thinks he can handle, but through his own growth and the help of his parents' friends, he is able to overcome this powerful antagonist.
It might be a new kind of monster created by the combination of Greek and Amazonian dark magic. This monster is immune to most normal weapons and has the strength to take on both Amazons and demigods easily. To defeat it, Percy comes up with a brilliant plan using his knowledge of both worlds, and Wonder Woman bows to him in admiration for his quick thinking and bravery in the face of this terrifying new villain.
Lex Luthor could be a great villain. He's always interested in taking down the Justice League and its affiliates. He might see the clone as a way to disrupt the Young Justice team and gain an advantage over Wonder Woman.
Lex Luthor could be a main antagonist. He might see their union as a threat to his power and schemes, and try to break them apart or use their relationship against them.