Well, one plot twist could be that Naruto discovers that the real villain is someone he trusted all along, like a respected elder in the village. Maybe this person has been secretly manipulating events to create chaos for their own gain.
Another plot twist could be that Naruto's detective work leads him to uncover a prophecy about himself that he was never supposed to know. This prophecy could say that he has a hidden power that, if awakened, could either save or destroy the ninja world. And this knowledge puts him in a difficult position as he has to decide whether to pursue it or keep it hidden.
Perhaps Naruto, while investigating a series of mysterious disappearances, finds out that there is a hidden underground organization that has the ability to use a special type of jutsu that erases people's memories. And this organization has ties to some of the most powerful clans in the ninja world. This would completely change the direction of his investigation and the story.
In this fanfiction, a possible plot twist is that Naruto's transformation into a Jashinist causes a rift in the ninja world. Some villages see him as a threat and form alliances against him. However, Naruto, using his unique perspective as a former Leaf ninja turned Jashinist, tries to bridge the gap between different ninja factions. He might also discover that Jashinism has a connection to an ancient prophecy that only he can fulfill, which changes how everyone views him and his new beliefs.
One plot twist could be that the princess is actually a spy. She was planted to be 'captured' so that Naruto would come to save her and lead the rescuers into a trap. But Naruto, being observant, notices some small details that give her away and he has to turn against her to save himself and his comrades.
One possible plot twist could be that Naruto sees a future where his friends turn against him. This would shatter his world as he values his friendships deeply. He might then struggle to figure out what went wrong in the future and try to prevent it in the present.
In this type of fanfiction, a cool plot twist could be that the Sound Ninja are not actually the bad guys. Naruto finds out that there has been a huge misunderstanding between the Leaf and the Sound. He then tries to bridge the gap between the two villages. Another idea is that Naruto is given a special mission by the Sound Ninja that has something to do with a powerful artifact hidden in Konoha. And the last one, what if Naruto is part of a prophecy in the Sound Ninja village that foretells of a great hero coming from outside their village to save them from a looming disaster?
Well, one plot twist could be that Naruto initially mistakes the guns for some strange new ninja tools. He might try to use them in his own unorthodox way, like combining his chakra with the gun's mechanism. Another could be that the guns are part of a plot by a new enemy who has somehow brought modern - day weapons into the ninja world. This would force Naruto and his friends to adapt to a completely different type of combat. Maybe Naruto would be the only one who could figure out how to stop these guns from being used against the village because of his unique ability to think outside the box.
Well, one possible plot twist could be that Naruto's hollow nature gives him unique powers. Maybe he can phase through objects like a hollow, which would be a huge advantage in battles. He could also have an inner struggle between his ninja self and the hollow side, similar to how characters in other stories deal with their dual natures.
Perhaps in this fanfiction, Naruto being born an Uchiha means he has a natural rivalry with Sasuke from the start. Since they both have Uchiha blood, they might compete not just for power but also for the right to be the true heir of the Uchiha legacy. Also, his Uchiha lineage could attract the attention of Orochimaru, who might see Naruto as a new vessel with the potential of the Uchiha powers.
One possible plot twist could be that Naruto, after learning more about Itachi's sacrifices for the village, starts to idolize him in a way that changes his own ninja path. He might adopt some of Itachi's stealthy and strategic techniques. For example, he could focus more on gathering intelligence before acting, rather than his usual head - on approach.
One possible plot twist could be that Konan discovers a hidden power within Naruto that even he doesn't know about. Maybe it's a connection to an ancient and forgotten jutsu. This could change the whole dynamic of their relationship and the way she saves him. For example, she might have to protect him not just from physical harm but also from those who would want to use this power for evil.
Maybe in this fanfiction, Naruto is exposed to a powerful dark jutsu that slowly corrupts his mind. As he becomes insane, he begins to abandon the values he once held dear. He could start using his powers for self - gain rather than for the protection of the village, like taking over control of Konoha in a tyrannical way.