The village elders or the ones who wrongly imprison Naruto also experience changes. They might start to doubt their decision as more evidence of Naruto's innocence surfaces. And in some fanfictions, this could lead to a reformation of the village's justice system. Overall, the false imprisonment of Naruto is a catalyst for a lot of character - driven plot developments in fanfiction.
For Naruto himself, it often shows his growth. He might be initially angry and frustrated at being wrongly imprisoned. But as the story progresses, he could become more determined to clear his name and prove his worth. It can also strengthen his bonds with his friends as they try to free him.
Naruto might initially be in shock and disbelief. He has always been loyal to the village, so being imprisoned for no real reason would be a huge blow. He would probably start by trying to reason with his captors, explaining that he is innocent. For example, he might say things like 'I've always protected this village, why would I do what you're accusing me of?'
There could be new characters created specifically for this fanfiction. Maybe a fellow prisoner who has some special knowledge or ability that helps Naruto during his imprisonment. Or a mysterious figure who is behind Naruto's false imprisonment, pulling the strings from the shadows.
One example could be a story where Naruto is framed for a crime he didn't commit by a hidden enemy within the village. This enemy manipulates evidence and convinces the village elders to imprison Naruto. Another could be a scenario where an impostor Naruto causes chaos and the real Naruto is wrongly accused and imprisoned as a result.
In this fanfiction, Naruto might endure the false imprisonment with dignity at first. Then, as his godlike abilities start to surface, he could use them to not only free himself but also to reform the prison system if it's corrupt. He could use his power to expose the false accusations and bring justice to those who wronged him.
In many such fanfictions, Naruto is initially hurt by the false accusations, especially if they come from his friends or the people he trusts in the village. But then, his strong will kicks in. He starts to analyze the situation carefully. He may talk to people who are neutral or try to find contradictions in the false accusations. He uses his ninja skills not just in combat but also in detective - like investigations to clear his name.
He could also be more resigned in some fanfictions. He might think about his past and how he's always been an outcast in a way, and see this imprisonment as just another hurdle. So, he would bide his time, waiting for a chance to prove his innocence.
For Naruto, if there's 'Trouble in Time', he might be separated from his friends. For instance, if time is distorted, he could end up in a timeline where Sasuke never returned to Konoha. This would deeply affect Naruto as his goal was always to bring Sasuke back.
In Naruto fanfiction, 'godlike doujutsu' often makes the characters who possess it extremely powerful. They can easily overpower their opponents in battles. For instance, they might be able to defeat powerful enemies with a single glance.
Hermione and Ron would surely be his top allies. They've been through so much with Harry and would stop at nothing to prove his innocence. Hermione's intelligence would be crucial in finding loopholes in the false charges and Ron's loyalty and courage would keep them going in the face of danger.
It can make characters act out of character. For example, a usually calm and collected ninja might become reckless when in love. They could take unnecessary risks to protect their loved one or to prove their love. This can put them in danger and also affect their reputation among their peers.