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.
Naruto could try to befriend the other inmates. Some of them might have useful skills like lock - picking or knowledge of the jail's layout. By working together with them, they could come up with a plan to escape. He could also use his charisma to convince the guards to let him out under false pretenses.
One reason could be that he was framed for a crime he didn't commit. Maybe some powerful enemy set him up to make him look like he attacked a village or stole a powerful artifact. Another possibility is that he broke some strict village laws in order to protect his friends. For example, if the village had a law against using certain jutsu without permission and Naruto used it to save someone, he could end up in jail.
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.
One possible reason could be that he's been framed for a crime he didn't commit. Maybe some powerful enemy managed to plant false evidence against him. For example, they could have made it seem like he attacked a village or stole a powerful artifact.
One possibility could be that Naruto emerges from jail with newfound powers. He might have been framed and while in jail, he discovers a hidden power within himself. He then uses this power to clear his name and also to protect the village from a new threat that emerged while he was incarcerated.
It could be a powerful ninja from another village who saw Naruto as a threat even when he was in jail. This ninja might have been plotting to take over Konoha while Naruto was out of the picture. Now that Naruto is out and godlike, they see him as an even bigger obstacle to their plans.
Well, it's a fan - created story related to Naruto. The 'limbo border jail' is likely a made - up or very niche concept within the Naruto fan world. It could involve Naruto or other characters facing new challenges in this jail. Maybe it's a place where villains are sent, and a story could revolve around a character trying to break someone out or deal with the chaos inside the jail.
His other friends like Shikamaru would use his intelligence. He would analyze the situation, figure out who is behind Naruto being thrown in jail, and then come up with a clever plan. He might gather the other members of the Konoha 11 and together they would work to free Naruto while also trying to expose the truth behind his imprisonment.
Since it's a fanfic, the main characters could vary widely. It might include some of the well - known Akatsuki members if the jail is somehow related to their activities. For instance, if the jail is a place where they keep their prisoners or secrets. Another possibility is that a new, powerful shinobi is introduced as the main character, who is on a quest to uncover the mysteries of the limbo border jail.