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.
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.
A cool plot twist might be that when Sasuke travels back in time, he finds out that his actions in the future were actually part of a grand plan set by an ancient Uchiha. So, all his attempts to change things are just following the script that was already written. Also, he could time travel to a time when the Uchiha were at the height of their power and he has to deal with the jealousy and suspicion of other clans who see him as a threat because they know what the Uchiha will become in the future.
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 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.
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.
One possible plot twist could be that Sasuke, upon traveling to the past, accidentally changes a small event that has huge ramifications in the future. For example, he might prevent a key encounter that led to a character's development, and as a result, the entire power balance in the ninja world is altered. Another twist could be that Sasuke's presence in the past is somehow detected by an ancient and powerful force, which then tries to either use him or destroy him. Or perhaps, Sasuke discovers that his own past self is not as he remembered, and there are hidden motives or secrets that he was unaware of before.
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 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 popular plot twist could be that Sakura discovers a hidden conspiracy behind the forced marriage. Maybe someone is using it to gain power in the ninja world. Another might be that Sasuke, initially cold towards the idea, starts to develop real feelings for Sakura during the process of the forced union, which changes the whole dynamic of their relationship.
They could also travel to a time during one of the great ninja wars. They might get involved in battles they previously only read about in history books. Sasuke could team up with his ancestors and Sakura could learn new medical techniques from the medics of that time. This would not only change the course of the war they are in but also bring back new knowledge to their own time.