It could be a former Leaf Village ninja who left due to some sort of disagreement. Maybe someone who didn't agree with the village's leadership or its way of training young ninjas.
The missing ninja could be a relative of a well - known character who has been in hiding all this time. They might come out of the shadows to train Naruto because they see a glimmer of hope in him for the future of the ninja world. For example, it could be a distant cousin of Minato or Kushina who has some special connection to the Uzumaki clan's powers and wants to ensure Naruto can fully utilize them.
Well, it depends on the nature of the missing ninja. If the missing ninja has a vendetta against the Hidden Leaf, they might train Naruto for their own malicious purposes. However, if they see potential in Naruto to bring about change, they could train him to be a better ninja in a more morally ambiguous way. Maybe they teach him stealth techniques that are not part of the normal ninja curriculum in the Leaf Village.
Naruto himself can be a popular character in 'naruto missing ninja fanfiction' in alternate scenarios. For example, if there was a plot where Naruto was somehow framed and had to go into hiding as a missing ninja. His friends would then be on a mission to find him and clear his name. Itachi is also quite popular. His self - sacrifice and his status as a missing ninja for a long time in the series can be explored further in fanfiction, like his possible secret plans or unfulfilled wishes.
One interesting 'naruto missing ninja fanfiction' could be about a missing ninja who has a secret power that no one knows. For example, he can control time in a very limited area. This power makes him a target for both good and bad forces in the Naruto world. Another could be a story where a missing ninja is actually on a quest to find a cure for a rare disease that is affecting his village, but he has to stay in the shadows to avoid being caught by those who misunderstand his motives.
It could be Orochimaru. He's always been interested in Naruto's power, especially the Nine - Tails within him. He might have come up with a new devious plan to capture Naruto and use his power for his own dark experiments.
She would likely be trained by some of the village's top ninja. Her father might get Kakashi or Gai to train her in combat skills. They would teach her how to use different ninja weapons and jutsu effectively.
One interesting masked ninja is Shinji. He is a masked character in fanfiction who was once a normal ninja but got cursed by an ancient evil. Now, with his masked identity, he tries to find a way to break the curse while also using his new - found dark powers for good in the Naruto world. There's also a masked ninja named Yuki. Yuki is a snow - style user and her mask is made of ice crystals. She is on a quest to find the origin of her ice - based powers. Another is Hikaru, a masked ninja with the power of light, who is often at odds with the darker elements in the Naruto fanfiction 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.
Kakashi could also be the main character in a different take on 'naruto rogue ninja fanfiction'. Imagine if for some reason, Kakashi was framed as a rogue ninja. He would have to use his intelligence and combat skills to clear his name while also dealing with the challenges of being an outcast. He might even discover some dark secrets about the Hidden Leaf Village in the process.
Perhaps it could be a powerful ice spirit that has been awakened by some dark jutsu. This ice spirit has no concept of good or evil but is causing destruction as it spreads ice everywhere. Naruto and his friends would have to find a way to either seal it or make it understand the harm it's causing. In this case, the ice spirit would be the main antagonist as it opposes the well - being of the villages.
The Leaf Village authorities could be the main antagonists. Since Naruto is now considered a rogue, they would be the ones trying to hunt him down. They might see him as a threat to the village's stability and security.