Perhaps Naruto is sent to prison as a form of political exile. In the prison, he discovers a dark conspiracy that is brewing. He has to find a way to break out and expose it. He might start by training some of the inmates who have potential in ninjutsu, creating a small force within the prison to oppose the corrupt guards who are part of the conspiracy. And all the while, he is constantly thinking of ways to get back to his village and clear his name.
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.
It could be that Naruto is imprisoned because he violated some ancient and archaic ninja law that no one really understands the origin of. In prison, he meets a mysterious old ninja who has been locked away for decades. This old ninja teaches Naruto some forgotten and powerful ninja techniques. Naruto then uses these new skills to change the prison environment for the better, from a place of despair to one of hope and redemption for the inmates, while also working towards his own freedom.
It could be that Naruto is sent to prison as part of a political move. There are some ninja clans within the village who are jealous of his popularity and influence. They conspire to get him out of the way by making it seem like he's a threat to the village's security. In prison, Naruto discovers a hidden conspiracy within the prison walls that is related to the outside political turmoil and he has to find a way to expose it while also getting himself released.
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.
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 he discovers some dark secrets in the Blood Prison. These secrets could be about the corruption of the ninja world or some hidden evils related to powerful people. This new knowledge might make him lose faith in the system he once believed in, leading to his transformation into a darker version of himself.
Well, one possibility could be that Naruto is wrongly accused of a crime in the Hidden Leaf Village and is sent to prison. There, he might meet other prisoners with unique abilities or stories. He could use his ninja skills in a different way, like trying to maintain peace among the inmates. Maybe he'd also be planning his escape while uncovering the real truth behind his false accusation.
One possible plot could be that Mikoto somehow survived and she takes Naruto under her wing. She trains him secretly, using her Uchiha knowledge to make him stronger. This could lead to Naruto having a unique set of skills that no one else has.
Well, one possibility is that Naruto resigns due to feeling burnt out from all the battles and political unrest in the village. He might decide he's done his part and wants a simple life away from the chaos.
Maybe Naruto discovers some dark secrets about his family that completely shatter his world view. For example, he finds out that his father was involved in some really bad things. This revelation makes him question everything he believed in and he becomes emo as a result. He might start wearing darker clothes, cutting off his hair, and his behavior towards others becomes cold and distant.
In a 'naruto is a uchiha fanfic', a possible plot could be that Naruto is so inspired by the Uchiha that he tries to bring back the glory of the clan. He starts by trying to understand their culture and values better. He could try to convince the village to support the revival of the Uchiha name. This would likely involve him dealing with the political aspects of the village as well as any lingering grudges against the Uchiha. He may also have to face off against those who would rather see the Uchiha stay in the past, all while learning more about the Uchiha's unique abilities and trying to incorporate them into his own fighting style.
There are probably 'naruto is evil' fanfics out there. A possible plot could be that Naruto is influenced by some dark force. This force twists his perception of right and wrong. As a result, he starts to target his former friends and allies. He might use his skills to cause chaos in the ninja world, believing that the current system is corrupt and needs to be overthrown.