A plot twist could be that Naruto loses his ability to use chakra in the middle of a big battle against a powerful enemy. Sasuke, Sakura, and Kakashi then have to find a way to not only protect Naruto but also defeat the enemy without relying on Naruto's usual strength. This would force them to develop new strategies and explore different aspects of their own powers.
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.
A great plot twist could be that Sasuke suddenly loses his sharingan and has to rely on his other skills and the help of the others. Naruto might have to train Sasuke all over again, and Hinata and Sakura could be involved in finding a way to restore Sasuke's sharingan. It would change the dynamics of their relationships and how they interact with each other.
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.
One interesting plot could be a story where Sasuke and Sakura have a child, and Naruto and Kakashi become like uncles to the child. They all live in the same village and face new threats together, with the new generation learning from the old. For example, the child might inherit Sasuke's sharingan and Sakura's medical skills, and Naruto and Kakashi help train the child to be a great ninja.
A plot twist could be that Sarada discovers she has a hidden power that neither Sasuke nor Sakura are aware of. It could be related to a long - lost Uchiha ability that skipped generations.
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.
Perhaps there's a Saiyan villain in the fanfiction who has the ability to manipulate time. This villain goes back in time and changes the events that led to Naruto and Sakura meeting. As a result, they grow up in a completely different world. Naruto might be more isolated without Sakura's initial friendship, and Sakura could be more focused on scientific research rather than being a ninja. When they eventually cross paths again, they have to overcome their differences and the changes in their personalities.
A really unexpected plot twist could be that the kidnappers are actually the good guys in a convoluted way. Maybe they know of a prophecy that Sasuke and Sakura are fated to bring destruction, so they are trying to stop it. Another idea is that during the kidnapping, Sasuke and Sakura end up in a different dimension where they have to rely on each other in completely new ways. Plus, the motives of the kidnappers could be related to a secret that Sakura has been hiding about her family all along.
A plotline could be that there is a powerful new enemy that specifically targets their bonds. This enemy uses illusions and mind - control to try and turn Sasuke against Naruto, or make Sakura distrust Kakashi. They have to fight not only the physical attacks of this enemy but also the mental and emotional turmoil it causes within their group. In the end, they realize the true strength of their relationships and are able to defeat the enemy.
One possible plot twist could be that Sasuke has been under a genjutsu that makes him target Sakura, and Naruto has to break the genjutsu first to truly save her. Maybe the one who cast the genjutsu is a new, powerful enemy who wants to disrupt the bond between Team 7. Naruto, with his strong will and newfound powers, manages to find the source of the genjutsu and free Sasuke from its control, thus saving Sakura from harm.
A plot twist could be that Akatsuki has a hidden agenda that Naruto, Sasuke and Sakura are unaware of when they join. Maybe Akatsuki is being controlled by an even more powerful and sinister force, and the three are lured in as pawns. They then have to figure out the real situation and fight not only against the Akatsuki members who oppose their reform ideas but also against this hidden power.