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 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.
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.
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.
One possible fanfiction could be about Sasuke becoming a missing nin again. Naruto and Sakura, now more powerful, set out to find him. They face many challenges on their journey, like dealing with other villages that want Sasuke for their own purposes. Naruto still believes in saving Sasuke from the darkness that led him to become a missing nin in the first place.
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.
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.
Danzo could be a great antagonist. He always had his own secretive and often unethical plans. He might see Naruto as a threat even if he's innocent and frame him as a missing - nin to get rid of him.
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.
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.