A rogue ninja from a long - forgotten clan who has a vendetta against the Hidden Leaf could be the main antagonist. This ninja could be the one who sets Naruto up as a missing - nin as part of a larger plan to destroy the Leaf Village.
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.
It could be a rogue hunter nin who doesn't like the idea of Naruto, an outsider, joining their ranks. This rogue hunter nin might see Naruto as a threat to their power and influence within the group.
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.
Kakashi could also end up being an ally. Despite his loyalty to the village, if he discovers the real reasons behind Naruto's departure and realizes that the village has made a mistake, he might choose to help Naruto secretly. He has a deep bond with Naruto and would not want to see him in harm's way.
Sasuke Uchiha could be a likely candidate. He had his period of being a rogue ninja. With his Sharingan powers, which allow him to copy jutsu and predict movements, and his own powerful ninjutsu like the Chidori and later the Rinnegan abilities, he would be a formidable opponent against the Kages.
Sasuke could potentially be an ally. Since they have a complex relationship, Sasuke might understand Naruto's situation and choose to side with him against the village. Also, characters like Jiraiya could still believe in Naruto and help him from the shadows.
They could be hunted by their former villages. Naruto, with his Uzumaki blood and powerful chakra, and Temari with her wind-based attacks, would have to constantly evade capture. Maybe they'd find a hidden place to hide and train, improving their skills even further. For example, Naruto could learn more about wind - natured chakra from Temari to enhance his Rasengan.
Sasuke could potentially be an ally. Given their complex relationship, Sasuke might understand Naruto's situation and choose to side with him. They have a deep bond, and Sasuke has also been an outcast in a way. Another could be Jiraiya. If he were still alive, he might believe in Naruto's innocence and help him from the shadows.
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 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.
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.