Perhaps Naruto is under the influence of a powerful and evil jutsu. This jutsu corrupts his mind to a certain extent and makes him do things that are against the village rules. The village then labels him as a missing nin. But as the story progresses, he struggles to break free from the jutsu's control and tries to prove that he's still the Naruto they once knew, all while being on the run from the village's ninja who are out to capture him.
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.
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.
Jiraiya might also side with Naruto. Jiraiya has always been a mentor and a father figure to Naruto. He would believe in Naruto's innocence and help him. He could use his connections and knowledge to keep Naruto safe and help him clear his name.
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.
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.
Isolation is a common theme. Since they are missing - nins, they are often alone and have to fend for themselves. Another theme is redemption. Many of these fanfics explore the idea of the missing nin trying to make up for their past mistakes.
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.
One idea could be that Naruto is forced to become a hunter nin after a rogue ninja from another village steals a powerful Konoha jutsu. He has to track the ninja down, using his unique skills like the Shadow Clone Jutsu for surveillance. Along the way, he discovers new chakra abilities that are specific to the hunter nin role.
A 'godlike missing nin naruto fanfic' can be interesting for several reasons. Firstly, the concept of a missing nin with such extreme power challenges the established power hierarchy in Naruto. It allows for new and exciting battles and interactions between characters. Secondly, the exploration of the character's backstory and how they became so powerful can be fascinating. It could involve some sort of ancient curse, a forbidden experiment, or a divine encounter. Finally, seeing how the existing Naruto characters react to this new and overwhelming threat or ally can create a lot of engaging storylines.
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.