Perhaps there is a spell or mind - control situation. A bad guy uses magic or some sort of mind - control device on Spider Man, making him do things that are against the law, and then he ends up in jail. He has to fight to break free from the control and prove his true self.
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.
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 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.
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.
In this fanfiction, Spider Man might struggle to keep his identity a secret at school. He could have to deal with normal school stuff like exams and bullies while also being a superhero.
Well, he could prevent some major tragedies. Maybe he stops the death of Uncle Ben all over again. This time he has the knowledge of the future and can avoid the mistakes that led to that fateful moment. It would change his whole character arc as he wouldn't be driven by that initial guilt.
Well, one possibility could be that they team up to fight a new super - villain in the city. Maybe this villain has some special powers that require both of their unique skills to defeat.
In fanfiction, perhaps Spider - Man discovers a hidden part of his powers. He might also have to deal with some personal issues at school while fighting bad guys. For example, he could be struggling with a difficult exam while also trying to stop a heist by a group of tech - savvy thieves. And his relationship with his friends could be put to the test as he tries to keep his identity secret from them.
Maybe Peter Parker faces a new and more powerful villain. For example, a super - intelligent criminal who can hack into any technology in New York. Peter has to use his wits and new skills he's developed since the first movie to stop him.