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.
A really engaging fanfiction could be where Naruto is trapped in a genjutsu -illusionary prison- which is made to look like a real imprisonment. The false imprisonment here is more of a mental and chakra -power- based one. He has to break free from the genjutsu which is made to seem like he's been wrongly jailed in the real world. His friends might not even be aware that he's in a genjutsu at first, adding more drama to the story.
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?'
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.
One example could be a fanfiction where Naruto is wrongly accused of stealing a powerful jutsu. In the story, perhaps a rival village's ninja frames him by planting false evidence at the scene. Another could be a situation where he is falsely accused of being a spy within his own village due to some misunderstandings and false testimonies.
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.
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 plot idea could be that Harry is framed by a powerful dark wizard who has infiltrated the Ministry of Magic. The wizard plants false evidence that makes it seem like Harry has committed a serious crime against the wizarding world. Harry then has to use his wits and the help of his true friends, like Hermione and Ron, to find a way to prove his innocence while being held in a magically fortified prison.
One possible reason could be a conspiracy within the village. Maybe some powerful and corrupt individuals in the Hidden Leaf want to get rid of Naruto for their own gains. They might frame him for a serious crime like treason or murder to eliminate his influence as a hero. Another reason could be a misunderstanding. For example, Naruto might be in the wrong place at the wrong time and there are false witnesses who claim he committed a crime he didn't. Or perhaps an enemy from outside the village has managed to create a false scenario that makes it look like Naruto is guilty in order to cause chaos within the Leaf Village.
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.
There's a 'izuku falsely accused fanfiction' where Izuku is accused of cheating during an exam at school. The story delves deep into how his classmates initially turn against him, but then slowly start to realize that there might be more to the story. It really plays on the emotions of the characters and readers alike.
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.