One possible plot could be that Naruto is framed for a crime he didn't commit. Maybe someone with a vendetta against him plants false evidence. In prison, he would have to deal with tough inmates and the strict prison regime while trying to prove his innocence.
It could be that Naruto is tricked into going to prison. He might think he's entering a special training ground or something. Once inside, he realizes it's a real prison. He then starts to make friends with the inmates, learning about their stories and hardships. He uses his positive attitude to bring some hope and change to the prison environment.
In a 'naruto goes to prison' fanfiction, it could be that Naruto is tricked into taking the blame for someone else. Once in prison, he meets old foes who are also incarcerated. Instead of fighting them, he tries to understand their motives and in the process, he uncovers secrets about their pasts that were related to some greater threat to the ninja world. This knowledge then becomes crucial for his future actions outside the prison.
The plot could involve Naruto being sent to the Blood Prison on a mission. Once inside, he encounters various types of ninjas with different abilities and motives. There could be a mystery surrounding a powerful and dangerous prisoner locked away deep within the prison. Naruto's journey in the Blood Prison could also be a test of his character, as he has to make difficult decisions about who to trust and how to handle the dangerous situations that keep arising. He may even learn some new jutsu from the inmates or discover a hidden power within the prison itself.
Maybe Danzo could be the main antagonist. He has always been a bit of a shady character in the Naruto series. He could see Naruto as a threat and use his influence to frame him and send him to prison to further his own political or power - hungry goals.
One possible plot could be that Naruto is wrongly accused of a crime he didn't commit. Maybe he was framed by an old enemy who wants to see him suffer. While in prison, he tries to prove his innocence. He could use his ninja skills subtly to gather evidence within the prison walls, and also make some unlikely allies among the inmates who start to believe in his innocence as they get to know him better.
In a 'naruto keeped in prison' fanfic, it could start with Naruto being framed for a crime he didn't commit by a mysterious enemy. Inside the prison, he faces all kinds of hardships. However, he uses his unique ninja skills, like his shadow clones in a very discreet way, to gather information. He could also form an alliance with other inmates who have different skills. Eventually, he uncovers the real culprit behind his imprisonment and clears his name while also making the village a safer place by revealing a hidden threat.
Maybe Naruto goes to hell to rescue a friend or to face some powerful dark forces. For example, he might go to save Sasuke who got trapped there somehow.
In a 'naruto goes rogue' fanfic, the plot could involve Naruto feeling betrayed by the Hidden Leaf Village. Maybe he discovers some dark secrets about the village leaders. For example, he might find out they were using him all along. So, he decides to break away and form his own group of outcasts who also felt wronged by the village.
Well, one possibility is that Naruto arrives at Beacon and his ninja skills make him stand out immediately. He could befriend Ruby and the others quickly, and they'd be amazed by his shadow clone jutsu. Maybe he'd help them train in new combat styles.
Well, it could be about Naruto going on a spiritual journey to meet Kami. Maybe he's seeking some sort of power or knowledge that only Kami can provide. He might face various challenges along the way, like powerful spirits or difficult terrains.
Well, it could be about Naruto arriving at Hogwarts and being confused by all the magic there. Maybe he tries to use his ninja skills in a world full of wizards and witches.