In a fanfiction where a missing - nin takes on the Kages, the story could go in many directions. The missing - nin could have a hidden agenda, like trying to steal a powerful jutsu or secret from the Kages. Maybe they were once a part of the village and had a grudge against the Kages. The Kages would represent the established order and power of the ninja world. Their fight would not only be physical but also a battle of ideologies. The missing - nin might be fighting for personal freedom or revenge, while the Kages are fighting to protect their villages and the stability of the ninja world.
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.
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.
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.
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 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.
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.
One common theme is redemption. Since Naruto is a missing nin, often the stories explore his path to redeem himself while building his harem. Another theme is power. His new status as a missing nin might give him different powers or ways to use his existing powers in the context of the harem.
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.