Well, sometimes in these fanfictions, a plot twist is that they time travel and end up swapping bodies. This adds a whole new layer to their relationship as they have to experience life from the other's perspective while also dealing with their yaoi - inspired feelings. Also, they might time travel to a future where their yaoi relationship has caused a major rift in the ninja world, and they have to go back in time to prevent that from happening. This forces them to confront their feelings and the potential consequences of their relationship much earlier than they would have in the normal timeline.
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.
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.
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.
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.
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 interesting plot twist could be that fem Naruto, instead of being the underdog like in the original story, is immediately recognized for her potential in the past due to her different appearance. Another could be that Sasuke, upon time traveling, tries to change things for the better but accidentally sets off a chain of events that makes the situation even worse. For example, he might try to stop certain tragedies from happening, but in doing so, creates new enemies or problems.
Perhaps Naruto travels back to a time when the Uchiha were at the height of their power. He then has to figure out how to deal with the Uchiha's more extreme members who are planning a coup. And in the process, he discovers a hidden connection between the Uchiha and an ancient evil that was long forgotten. This connection could change everything he thought he knew about the Uchiha and the ninja world in general.
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.
One common plot twist is that Kurenai, instead of being a bystander in some historical events in the Naruto world, becomes a key figure in changing them during the time travel. For example, she might prevent a certain character's death that had a major impact on the original storyline. Another plot twist could be Naruto discovering a hidden power within himself only when he travels back in time, which was not accessible in his original timeline. And sometimes, the time travel itself is not a one - way trip, and there are complications in getting back to their original time, adding more suspense to the story.
One popular plot twist could be Mito Uzumaki traveling back in time and accidentally changing the events that led to the Uzumaki clan's downfall. This could create a whole new set of challenges and opportunities for the characters in the Naruto universe.