Another plot twist could be that the Akatsuki are not actually the villains they seem. They are a group formed to protect a greater threat that the hidden villages are too blind to see. Naruto discovers this and has to convince his village to work with the Akatsuki, which would be a huge change in the typical Naruto narrative.
One interesting plot twist could be making Naruto an outcast not just because of the Nine - Tails, but because of a secret power he unknowingly has that is feared by the village elders. This would add a whole new layer to his struggle for acceptance.
Perhaps in this fanfiction, Sasuke could be the one to initially understand Naruto's power and instead of being rivals, they become allies much earlier. Sasuke could then help Naruto train this power in secret, which would completely change their relationship dynamics and the story's flow.
The leviathan could be part of a prophecy that Naruto doesn't fully understand at first. When he summons it, he discovers that the leviathan's actions will either save or destroy the ninja world, depending on what Naruto does next. This creates a high - stakes situation and a great plot twist.
One interesting plot twist could be that Naruto discovers he has a hidden power from a long - lost clan that changes the course of the final battle. This power might be something that gives him an edge against a seemingly unbeatable foe.
A great plot twist could be that Naruto turns out to be a half - vampire. It would completely change his character arc and how others in the Naruto world perceive him.
A possible plot twist could be that Naruto's blindness was actually caused by an enemy's secret jutsu that was meant to be permanent, but it turns out that Naruto's Uzumaki bloodline has a hidden ability that can reverse the blindness under certain conditions. This would add an element of mystery and hope to the story.
In some fanfictions, a character from Naruto might end up with a Devil Fruit power from One Piece, which is a huge plot twist. For example, Sasuke getting the Logia type Akuma no Mi. It completely changes his fighting style and how he interacts with the world.
In 'Naruto Chance to Change Fanfiction', a storyline could involve Naruto having the chance to change his relationship with Sasuke. He might be able to stop Sasuke from leaving the village in the first place. This would then change the entire dynamic of their rivalry and friendship. Also, he could use this chance to change how the Akatsuki is formed or dealt with, perhaps by finding a way to reform some of its members.
Imagine a plot twist where the Sharingan and Rinnegan are not unique to the ninja world. In a fanfiction, it could be revealed that an alien race has similar powers. A character from Naruto's world travels to this alien planet and discovers that their understanding of these powers is completely different. They must then adapt to this new knowledge and use it to save both worlds from a common enemy that is drawn to the power of the Sharingan and Rinnegan.
One interesting plot twist could be that Naruto discovers he has a long - lost sibling from a different village. This would completely change his perception of his family and his place in the ninja world.
One interesting plot twist could be that Neji discovers a new power within his Byakugan that makes him evenly matched with Naruto's Nine - Tails power. Maybe he unlocks a hidden ability that allows him to see through Naruto's chakra cloaks or disrupt the Nine - Tails' chakra flow. Another plot twist could be that Naruto loses his access to the Nine - Tails' chakra during the fight, and has to rely solely on his own skills and training, making it a much more even match against Neji.
There could be a plot twist where Ayame turns out to be a key figure in an ancient prophecy related to the Hidden Leaf Village. Her marriage to Naruto is part of fulfilling that prophecy, but there are forces that don't want this to happen. So they try to stop the wedding. This could lead to a series of battles and challenges that Naruto and Ayame have to face together, ultimately strengthening their bond in the process.