Perhaps Gotham City is under a new regime that views Batman as a vigilante causing more harm than good. They pass laws to arrest any masked vigilantes, and Batman, being the most prominent one, gets caught. In jail, he meets old enemies who are also locked up. He then has to find a way to escape while also trying to make the new regime see the importance of his work in keeping Gotham safe.
It could be that Batman breaks one of his own moral codes in a desperate situation. For example, he might accidentally cause the death of a criminal while trying to stop a major crime. This action, which goes against his no - killing rule, makes the public and the law turn against him, sending him to jail. In jail, he has to face his own inner demons and also deal with the threats from other inmates who see him as a big target.
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.
Well, perhaps Naruto accidentally breaks a really important and ancient law in the ninja world. It could be something related to a forbidden jutsu that he was unknowingly involved in. As a result, he's thrown into jail. There, he might start to reflect on his actions and ninja way, and also try to find a way to prove his innocence while making some unexpected allies among the prisoners.
In a 'Harry Potter goes to jail' fanfiction, perhaps Harry breaks a new law that the Ministry of Magic has created to maintain control. For example, if he tries to teach magic to non - magic people in an attempt to prepare them for a potential dark wizard threat. The Ministry, fearing chaos, throws him in jail. Inside, he meets other wrongly - imprisoned wizards and they plan an escape together while also fighting against the unjust system.
Maybe he was framed by a powerful villain. The villain planted evidence to make it seem like Spider Man committed a serious crime, and without a chance to fully prove his innocence right away, he was sent to jail.
One possible plot could be that evidence of their abuse towards Harry finally surfaces. Maybe a wizarding neighbor who has been secretly observing them reports their cruel treatment of Harry to the wizarding authorities. Then they are arrested and sent to a wizarding jail, where they struggle to adapt to the magical world's justice system.
It could be Danzo. He's always been a bit of a shady character in the Naruto series. He might see Naruto as a threat to his power and influence in the village. So, he could frame Naruto for some crime and get him sent to jail just to eliminate his competition.
Perhaps Percy is in jail as a sacrifice for someone he loves. In the fanfiction, he might be accepting his situation at first, but then his friends outside start to plan a rescue mission. It could show his loyalty and their determination to get him out.
One possible plot could be that Edward is wrongly accused and is in jail. His friends outside start an investigation to prove his innocence. They might face many obstacles like uncooperative witnesses or a corrupt system.
Maybe he would use his detective skills to solve school mysteries, like finding out who stole the cafeteria's best cookies.
The main antagonist could be a new character, a corrupt official in the Ministry of Magic who wants to get rid of Harry because he's seen as a threat to their power. This person could manipulate the legal system to send Harry to jail.