Well, some storylines could center around a missing nin's relationship with other outcast characters. They might form their own group outside the traditional ninja structure. For example, a missing nin could team up with other rogue ninjas to take on a greater evil that the established ninja villages are ignoring. Or perhaps a missing nin has a past connection to a main character like Naruto, and the story delves into how that affects the Naruto's journey and his view on the concept of missing nin.
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.
Another idea is that Naruto and Hinata go missing - nin to explore a dark power that is threatening the ninja world but is being ignored by their village. They sacrifice their status in the village to do what they think is right. Their relationship deepens as they face the difficulties and moral dilemmas together.
Sasuke is often a popular character in such fanfictions. His initial departure from the village makes him a prime example of a missing - nin. Writers like to explore his journey further, what he experiences outside the village, and how his relationships change.
Sasuke Uchiha is often a popular S - rank missing - nin in fanfiction. His defection from Konoha makes him a prime candidate for such stories. Orochimaru is another. His thirst for knowledge and power led him to become a missing - nin, and his abilities and mysterious nature are great fodder for fanfiction. Then there's Kakuzu. His unique jutsu and long life as a missing - nin give writers a lot to work with.
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.
Sasuke is often a popular one. In fanfiction, his journey as a missing - nin and potential connection to Akatsuki can be explored in many ways. His power and his complex relationship with Naruto make him a fascinating character to write about in this context.
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.
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.
Perhaps the missing nin discovers new abilities within the Rinnegan that no one else has. They might be able to combine different paths in unexpected ways. For instance, using the Animal Path to summon creatures and then enhancing those creatures with the power of the Asura Path. This would make their summoned beasts more powerful and difficult to defeat in combat.
One interesting storyline could be a medic nin who discovers a new healing jutsu during a war and has to protect it from enemy ninjas. Another could be a medic nin's journey to heal a cursed ninja. There could also be a story about a medic nin training under Tsunade and facing various challenges in the process.
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.