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.
Gaara could be an ally. Gaara has his own experiences of being an outcast in the past. He might empathize with Naruto and offer his assistance. Also, some of the minor characters who have always been on the fringes of the village and have a sense of justice might join Naruto. For example, those who have seen the corruption within the village first - hand.
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.
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 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.
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.
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.
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.
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 be one of his allies. Despite their past differences, Sasuke might see Naruto's new path as a way to create a better world. He could offer his combat skills and strategic mind to help Naruto rule. Another ally could be Hinata. She has always been supportive of Naruto, and as emperor, Naruto would need someone he can trust, and Hinata fits that role perfectly.
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.