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.
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.
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 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.
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.
The Kingpin could be a likely antagonist. He has the resources and the motive to frame Spider Man and get him out of the way. He could use his criminal connections to plant false evidence and make sure Spider Man ends up in jail.
It could be a new dark wizard who has some personal vendetta against Harry. Maybe this wizard has a grudge because Harry defeated Voldemort and he wants to prove he's more powerful, which enrages Harry and causes him to go on a rampage.
It could be a new dark wizard who has the power to manipulate minds. This wizard might target Harry specifically, driving him insane as part of a larger plan to take over the wizarding world. Since Harry is seen as a hero, if he goes insane, it would create chaos and make it easier for the antagonist to achieve his goals.
There could be a dark entity that lurks within the Durmstrang castle itself. It might have been awakened by Harry's arrival or has some connection to the school's past. This entity could manipulate students and teachers alike to create chaos and oppose Harry.
Obviously, the Dursleys themselves are the main antagonists. Vernon Dursley, with his short temper and extreme dislike for anything out of the ordinary, could be the driving force behind Harry's death. He's always been shown to be cruel to Harry in the original series. Petunia Dursley, too, could play a major role. Her envy of her sister and her hatred for Harry could lead her to either directly cause his death or be complicit in it. And Dudley, with his spoiled and bullying nature, might also be a key figure in Harry's demise.
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.