Commissioner Gordon might also take on the role of the main antagonist. He has always been an ally of Batman, but if Batman goes evil, Gordon would have to use all his resources and his understanding of Gotham's underworld to try and stop the Dark Knight. He could form a special task force dedicated to taking down the now - evil Batman.
The Bat - family members like Robin or Nightwing could become the main antagonists. They would be horrified by Batman's transformation and would try to stop him from causing more harm. Their knowledge of Batman's tactics and his lair would be their advantage in trying to bring him back to the side of good.
Another possibility is that a new hero or anti - hero could emerge as the main antagonist. Someone who sees the threat that an evil Batman poses to Gotham and decides to take matters into their own hands. This could be a character who has been in the shadows of Gotham all along and now steps into the spotlight to face the corrupted Dark Knight.
The Joker could be the main antagonist. Even though Batman is in jail, the Joker could find a way to continue his chaos - making. He might try to get into the prison to torment Batman or use the situation to his advantage by causing mayhem in Gotham City without Batman there to stop him.
The Batman Who Laughs could also serve as the main antagonist. He represents a twisted version of Batman, and his goal could be to infect all the Batverses with his madness. His knowledge of Batman's tactics and his own insanity would pose a huge challenge for the normal Batman as he tries to stop him from spreading chaos.
The Joker could be a likely main antagonist. He might be the one who manipulates the situation to get Batman arrested, perhaps by framing him for one of his own heinous crimes. The Joker loves to play mind games, and getting Batman locked up would be a huge part of that.
The Joker is always a great choice. He could come up with a particularly cruel and elaborate plan to put Batman in peril, like kidnapping all of Batman's allies and forcing him to choose which ones to save.
Darkseid could be a potential main antagonist. He might view Superboy as a weapon that he wants to control. If he realizes that Batman is trying to shape Superboy into a hero of Earth, he would surely try to stop it. He could send his minions to attack Batman and Superboy or try to corrupt Superboy's mind from afar with his Omega Beams.
It could be a new villain created specifically for this fanfiction. Maybe a powerful ninja - like figure from another dimension who is jealous of Naruto's powers and wants to take them for himself while Naruto is in the Batman universe and feeling neglected, so he has to fight this new threat alone at first.
The Joker could still be the main antagonist. He might find the idea of Batman being a girl extremely hilarious and try to use it to his advantage. Maybe he would try to play mind games with her, thinking that she would be more vulnerable in her new form.
The main antagonist could be a deranged chemist who was once shunned by the scientific community. He uses his knowledge of chemistry to create deadly toxins and gases to get revenge on those who wronged him. He sees Batman and Robin as obstacles in his path of destruction.
Ink could be a great antagonist. He has the ability to manipulate his body into various weapons and forms. He could be seeking to take over Gotham's underworld in the 'Batman Beyond' era and sees Nightwing and Batman Beyond as threats to his plans.
The Joker would be a great antagonist. He could be the one who creates the situation where Batman is in a diaper, perhaps as part of some elaborate and twisted prank. He'd find it hilarious to see the Dark Knight in such a vulnerable state and would use it to his advantage to cause chaos in Gotham.