Well, a possible plot twist is that when they travel back in time, Sakura loses her medical skills. This forces her to learn them all over again in a more difficult environment in the past, and in the process, she discovers a new way of using medical ninjutsu that she brings back to the future. As for Kakashi, his Sharingan might behave differently in the past due to some temporal anomaly. This could lead to him having to control a new and unexpected power while also dealing with the enemies from that era. Also, they might find out that their time travel was actually set up by an enemy who wants to use their presence in the past to change the future to their advantage.
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.
Imagine a fanfiction where Sakura, instead of being in love with Sasuke, has feelings for Naruto all along. This would completely change the love triangle aspect and lead to a lot of interesting interactions between the three main characters. It could also cause Sasuke to re - evaluate his relationship with his teammates.
They could time - travel during a great war in the past. Kakashi and Sakura might find themselves in the middle of battles they only read about in history books. They could use their modern - day skills to change the outcome of certain battles. This would also have a huge impact on the present - day Naruto world as they know it.
One idea could be that Sakura, as an Anbu, travels back in time and tries to prevent certain tragedies in Kakashi's past. Maybe she stops Obito from 'dying' initially, which would change the entire Naruto storyline in a major way.
In a Sakura and Kakashi time travel fanfiction, they could end up in the past during a major war. Kakashi would be a great asset with his Sharingan and combat skills. Sakura, on the other hand, could help the wounded soldiers. Their presence in the past could change the outcome of the war. For example, they might be able to save some important characters who were supposed to die. This would then lead to a completely different future when they return to their own time.
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.
One possible plot twist could be that when they travel back in time, they accidentally change a small event that has huge consequences in the future. For example, they might prevent a key meeting between two clans, which then alters the political landscape of the ninja world. Another could be that they find out that one of them was actually from that time originally and had their memories wiped in the future. This would completely change their understanding of themselves and their place in the ninja world.
One interesting plot twist could be that Naruto, with his knowledge of the future, tries to prevent certain tragedies but ends up causing new ones. For example, he might try to save a character too early and disrupt the natural flow of events, leading to unforeseen consequences.
One possible plot twist could be that Sakura, during the time travel, accidentally alters the past in a way that instead of Madara becoming a villain, he becomes a hero. This change could completely shift the future she came from. For example, if she prevents Madara from finding certain power sources or meeting certain people who influenced his dark path, it could lead to a very different Naruto world. Maybe he would use his strength to unite the clans in a more peaceful way, and Sakura would then have to figure out how to return to her own time in this new timeline.
One possible plot twist could be that they travel back to a time when their friendship was on the verge of breaking. They then have to navigate their past selves' insecurities and rivalries all over again, but this time, with the knowledge of how important their friendship is in the future. This could lead to some really heart - warming moments as they try to fix things before they go wrong.