Another interesting angle is a missing - nin who discovers a long - lost ninja art outside the village. They then use this new - found power to either seek revenge on those who drove them out or to protect the ones they love who are still in the village. For example, they could master a unique form of shadow - based jutsu that was lost in history.
Maybe Naruto goes missing - nin by choice to protect the village from a secret and powerful threat that he can't fight as an official shinobi. He could be secretly training in isolation and gathering allies from the fringes of the ninja world.
In a 'naruto is a missing nin fanfiction', Naruto could be forced to become a missing nin due to a threat against his friends. He leaves to draw the danger away from them. While on his own, he trains intensively and becomes a more powerful and stealthy ninja. He also has to deal with the emotional turmoil of being separated from his loved ones and the village he once called home.
Kimimaro could be an interesting missing nin character to explore in fanfiction. He was a tool for Orochimaru, but had his own internal struggles. You could write about his life before fully becoming a missing nin, his loyalty to Orochimaru despite his own deteriorating health, and what might have happened if he had broken free from Orochimaru's control. Another character could be Nagato. Before he became Pain, he had experiences that could be considered as leading towards a missing - nin - like existence. His views on peace and his use of the Akatsuki could be delved into in the context of a missing nin story.
A great fanfiction idea could be that Sakura becomes a missing nin after an incident in the village. Naruto and Sasuke, who have their own issues, must now work together to find her. Along the journey, they realize how much they need Sakura in their lives and also discover some secrets about the village that made Sakura leave. This would be a story of self - discovery and friendship.
One idea could be exploring the backstory of an S - class missing - nin. Maybe they had a noble reason to turn their back on the village at first, like trying to protect a loved one from a corrupt system within the village.
Well, a plot might involve an S - rank missing - nin who was framed. They are hunted by all the villages but are actually innocent. As they try to clear their name, they uncover a conspiracy within the ninja world. Another interesting plot could be an S - rank missing - nin who has a unique ability that no one else has. This ability makes them a target, but also gives them the power to change things. For example, they might be able to control a powerful natural force like a storm or an earthquake. And then there's the idea of an S - rank missing - nin who is on a quest for revenge against a particular village or person, but as they pursue their revenge, they start to question whether it's really worth it.
One plot idea could be a missing - nin from Naruto who joins Akatsuki but secretly plans to undermine them from within. Maybe they have a personal vendetta against one of the Akatsuki leaders. Another idea is a missing - nin's journey of redemption while being part of Akatsuki. They could start to question the group's motives and try to find a way out without getting killed.
One idea could be a missing - nin who was once a friend of Boruto's and has some unique jutsu. This missing - nin could be on a quest to find a cure for a rare disease that his family has. Boruto, upon learning of this, has to decide whether to bring him back as a missing - nin or help him.
One popular storyline could be about a missing nin who has a change of heart and tries to secretly protect the Hidden Leaf. Another might involve a missing nin with a unique power that the various ninja villages are trying to either recruit or eliminate. There could also be stories where a missing nin is on a quest for redemption after being wrongly accused.
If Naruto and Temari were missing nin in a fanfiction, it could start with a misunderstanding. Naruto might be framed for a crime he didn't commit and Temari, believing in his innocence, decides to help him escape. They then have to live on the run. Along the way, they meet other outcasts and form a sort of rebel group. Naruto's ability to make friends easily and Temari's strong leadership skills could be the driving force behind this new group's growth.