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.
One scenario could be that an outside force, like a powerful and evil organization, frames Naruto and Temari to cause chaos in their villages. So they have no choice but to flee as missing nin. During their time on the run, they discover the true intentions of this organization and decide to fight back. Their journey would be filled with battles, self - discovery, and the strengthening of their bond as they face numerous difficulties together.
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.
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.
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.
In a 'naruto becomes a missing nin fanfiction', perhaps Naruto discovers some dark secrets about the village leadership. These secrets are so dangerous that the village wants to silence him. He then decides to go rogue to expose these secrets to the world. As a missing nin, he might form alliances with other outcasts who also have a grudge against the current system.
Well, one possibility is that Naruto leaves the village due to being wrongly accused. He then has to survive on his own while being hunted as an S - rank missing nin. He might form unexpected alliances with other outcasts and use his unique skills in new ways.
A great plot idea would be that the missing nin with the Rinnegan is actually a good - hearted person who was framed. They use their Rinnegan powers not for evil but to prove their innocence. Along the way, they encounter other ninjas who gradually come to understand their situation and start to help them. This could include forming alliances and fighting against the real villains who set them up.
In this fanfiction, Naruto might gain new and stealthy abilities as a Hunter Nin. He could be tasked with tracking down dangerous rogue ninjas. His skills in stealth and assassination, which are not typically associated with his regular character, would develop. This would add a new layer of complexity to his character and the Naruto universe in general.
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.
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.