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.
In such a fanfic, it could be that Naruto discovers some dark secrets about the village leadership. These secrets are so dangerous that the leaders try to silence him. Naruto refuses to be silenced and decides to break away from the village, becoming a missing nin. He then travels the ninja world, gathering allies who also believe in exposing these secrets and fighting against the unjust system of the village.
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.
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.
A possible plot twist could be that the missing - nin is being controlled by a greater evil. Naruto, being raised by this missing - nin, unknowingly gets caught up in a much larger conspiracy. As he grows up, he starts to notice strange things about his guardian and eventually discovers the truth, leading him to have to make some tough decisions about loyalty and what is right.
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.
If Naruto becomes a Suna Nin in fanfiction, the plot would change drastically. For one, his relationships with characters in Konoha would be strained. His bond with Sasuke might take a different turn as they would be on opposing sides. Also, Naruto would have to adapt to Suna's culture and ninja techniques. He might learn new jutsus specific to the Sand Village, which could make him an even more formidable ninja in a different way than he was in Konoha.
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.