In some fanfictions, a great plot twist is when they travel back to the time of the Sage of Six Paths. Naruto and Sasuke find out that they were part of a much larger plan that the Sage had all along. This changes their perception of their own fates and the history of the ninja world. They now have to decide whether to follow the Sage's original plan or create their own path, all while trying not to disrupt the flow of time too much.
Maybe they travel back to their early days at the ninja academy. Naruto, who now has all his future knowledge, tries to befriend Sasuke in a different way. But Sasuke, being suspicious, thinks Naruto has some ulterior motive. This leads to a whole new set of comical and at the same time tense interactions between them as they both have to deal with their past selves and the changes they want to make.
A common plot twist is that during their time travel, they find out that they are fated to be together in a yaoi relationship in all timelines. So, they have to figure out how to make it work in the past while also dealing with the knowledge that they are from the future. It could also be that the time travel is caused by a powerful yaoi - themed magic or jutsu that has some unforeseen side effects, like making them more in tune with each other's emotions on a romantic level, which then leads to all kinds of interesting interactions and decisions as they navigate their past and future.
One interesting plot twist could be that in the time - travel, Naruko accidentally changes a key event that makes Sasuke a completely different person. Instead of being brooding and revenge - driven, he becomes more light - hearted and focused on building a new, peaceful shinobi world. This forces Naruko to re - evaluate her relationship with him.
One interesting plot twist could be that the Sannin travel back to a time when Orochimaru was still a good - hearted ninja. They could try to prevent his fall to the dark side. This would change the entire future of the Naruto world as Orochimaru's actions had a huge impact on many events.
Perhaps a really cool plot twist is that the time travel was actually a trap set by an old enemy. When Kakashi and Naruto travel back, they find out that this enemy has been manipulating events from the past all along. They then have to not only fix the past but also figure out a way to stop this enemy from using the past to destroy their future.
Well, a cool plot twist could be that Naruto and Mito time travel to a period right before the Nine - Tails was sealed in Mito. Naruto, with his knowledge of the future, tries to find an alternative way to deal with the Nine - Tails' power. This could completely change the history of the Uzumaki clan and the Hidden Leaf. Also, they could time travel to a time when the first Hokage was still alive and Naruto has to convince him of future threats without revealing too much. Or perhaps they travel to a time when a powerful enemy was about to attack the village, and they use their future skills to defeat the enemy in a way that shocks everyone in the past.
One interesting plot twist could be that Naruto travels back in time and discovers that the Hidden Leaf Village was founded on a much darker secret than he ever knew. This changes his perception of the village's history and his role in it.
Another popular plot twist is that when they travel back, they find out that the past isn't exactly as they remembered it. There could be some hidden secrets or different motives of the characters they thought they knew well. For instance, they might discover that a certain villain had a more complex backstory and wasn't always evil. This changes their perspective on how to deal with things in the past and future.
One popular plot twist is when they travel back and find out that the events they thought they could easily change are actually much more complex due to some hidden forces at work. For example, in some fanfics, they discover that an ancient jutsu is behind all the chaos and they have to find a way to break it.
A great plot twist could be that they time travel into the bodies of their younger selves but with their current godlike powers. They then have to deal with the reactions of their friends and family who don't understand what has happened to them, while also trying to use their new - found situation to prevent some future disasters.
In some Sakura and Sasuke time travel fanfictions, a great plot twist is that they time travel to a point where they meet their younger selves. This can lead to some really complex and emotional situations. The younger Sasuke might not trust the future Sasuke, thinking he's an imposter or has been corrupted. The same could go for Sakura. Another plot twist could be that the time travel is caused by a forbidden jutsu that Sakura accidentally activates. And as they travel through time, they start to lose their memories bit by bit, adding a sense of urgency to their journey to get back to their own time and figure out what's going on.