One possible new character could be a young orphan with a hidden talent for ninjutsu. Naruto, having been an orphan himself, takes the kid under his wing. This new character could have a unique power that is related to illusions but in a much more advanced and dangerous way than the normal genjutsu. Another new addition could be a ninja from a rival village who, after seeing Naruto's growth, decides to join him instead of fighting against him. This character could bring with him the knowledge of the rival village's secret ninja strategies.
Well, one possibility is that Naruto feels betrayed by the Hidden Leaf Village. Maybe they wrongly accused him of a serious crime. So, he decides to go rogue. He could then start traveling alone, using his skills to survive and avoid capture. He might also meet other outcasts who understand his situation.
One idea could be that Naruto is sent on a mission to the Hidden Mist Village and gets separated from his team. He then has to adapt to the Mist Ninja ways to survive. He might learn their unique jutsu, like some water - based techniques, and form unexpected alliances with Mist Ninja who admire his determination.
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.
In this fanfiction, Naruto might gain new and unique ninja skills. Maybe he discovers a long - lost jutsu that makes him even more powerful than in the original story.
Perhaps there could be some of Kaguya's old allies or servants who come back to serve Naruto. Or new villains who are related to Kaguya's past enemies.
In certain fanfictions, the main antagonist might be a powerful alien - like being that arrives on Earth (in the Naruto world). This being has technology and powers that the ninjas have never seen before. It views Naruto as a symbol of the resistance against its invasion. Also, there could be an antagonist who is a master of genjutsu, far more powerful than any seen before, and he uses his illusions to try and break Naruto's spirit and stop him from becoming the strongest ninja.
Sasuke can also be a popular character in Naruto Ronin Ninja fanfiction. He might cross paths with Naruto during his ronin days, and their relationship could be explored in new and interesting ways. Maybe they have to team up again to face a common enemy, or they might be on opposite sides for a change.
Zabuza Momochi is quite popular. His unique sword - wielding skills and his complex relationship with Haku make him a great character for fanfiction. Writers often explore his backstory more deeply or create alternate scenarios where he survives and has further adventures.
Naruto himself is obviously a very popular character in this type of fanfiction, given that it's about a 'naruto cyborg ninja'. Sasuke could also be a popular character, perhaps as an adversary or an ally to the cyborg Naruto, depending on the plot.
Naruto himself is often a central and popular character in such fanfiction. His natural determination and growth as a ninja make him an ideal focus for stories about a prodigy.