One interesting plot twist could be that Naruto discovers a new, hidden power within himself that has been dormant all this time. Maybe it's related to an ancient Uzumaki clan ability that was lost but resurfaces in this flash - forward scenario. This new power could change the balance of power in the ninja world.
Perhaps in the flash forward, the relationships between the characters have drastically changed. Sakura could have become a rogue ninja for some reason, and Naruto has to choose between his loyalty to the village and his friendship with her. This would create a huge moral and emotional conflict for Naruto.
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.
Another plot idea might be centered around a young ninja who is born with a natural affinity for the Black Flash but has to overcome many obstacles and rivalries in the ninja world to master it fully. This could involve facing off against older, more experienced ninjas who are jealous of this natural talent.
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.
A great plot twist might be that some of the villagers who were thought to be innocent are actually in cahoots with Pain. They could have been secretly helping him all along, providing information or weakening Konoha's defenses from the inside. This would shatter Naruto's perception of the village and add a lot of drama and conflict to the story as he has to deal with both external and internal enemies.
Maybe the different teacher is actually a time - traveler. This teacher has knowledge of future events and tries to train Naruto in a way that will prepare him for things that haven't happened yet. For example, training him to fight against a new type of enemy that no one in the current time has even heard of. It would completely change the dynamic of Naruto's growth and the story's progression.