Ra's al Ghul could also be the main antagonist. He has different views on how to save the world compared to Batman. He might use his influence and resources to have Batman arrested so that he can carry out his own plans for Gotham or the world without Batman interfering.
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.
A new dark wizard or witch could be the main antagonist. This character, jealous of Harry's fame and power, creates a situation where Harry is framed for a heinous crime. They then ensure his arrest so that they can take over the role of the 'chosen one' in the eyes of the wizarding public and start spreading their own brand of dark magic.
It could be a jealous rival. This rival might be envious of mankae's popularity or achievements. So, they set him up to get arrested by providing false information to the police. They want to see mankae's downfall and think that getting him arrested is the best way to achieve this.
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 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.
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.
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.