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.
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.
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.
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.
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.
It could be a new character, perhaps a corrupt wizard in the Ministry of Magic who has a vendetta against the Dursleys for some reason. This wizard might make their time in jail even more difficult by withholding basic rights or subjecting them to unfair treatment. And he might be doing all this for his own gain, like trying to steal the Dursleys' Muggle money or something.
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.
Well, perhaps Harry Potter goes to Dalton and discovers a whole new world of magic there. Maybe he meets new friends and has to face different challenges compared to Hogwarts.
In this fanfiction, it could be that Harry Potter has a vision of a future where Voldemort has completely taken over the wizarding world and killed all his loved ones. This drives him into a state of madness and he goes on a rampage. He travels back in time using some ancient magic he discovers, and starts to take out all the Death Eaters one by one, not caring about the consequences, as he believes it's the only way to change the future.
One possibility could be that after facing too many dark magic encounters, Harry's mind starts to break. Maybe the constant threat from Voldemort and the losses he endures, like the death of his friends, push him over the edge. He could start to have hallucinations and lose his ability to distinguish between reality and dark magic-induced illusions.
Maybe it's about Harry Potter being framed for using dark magic in a way that violates the wizarding laws. As a result, he has to go to this 'juvie' place. In there, he discovers that there are other kids who have also been wrongly imprisoned. He then uses his skills and the loyalty of his friends (who might try to break him out or help him legally) to fight against the unjust system.