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.
Hidan is another. His unique abilities and his rather wild personality make for interesting stories. In fanfiction, a missing - nin might be intrigued by Hidan's immortality and either try to learn from him or try to stop him from causing more chaos in the name of Akatsuki.
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.
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.
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.
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.
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.
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.
Naruto is obviously very popular as he is the main character of the original series. His interactions with the Akatsuki members are always a focal point in fanfictions.