One interesting plot twist could be that female Naruto, with her knowledge of the future, tries to prevent Madara from making certain mistakes that led to his downfall in the original timeline. For example, she might show him the true nature of the power he was seeking, making him question his motives.
Well, a cool plot twist might be that Fem Naruto has a secret lineage related to Madara's own clan. Maybe she discovers this and it makes Madara question his long - held beliefs and grudges. Or perhaps in the fanfiction, Fem Naruto is able to use a new form of ninjutsu that is a combination of Uzumaki and Uchiha techniques, which she uses to outwit Madara in a crucial battle. It could also be that Madara's real goal was to actually find a successor like Fem Naruto all along and his actions were just a test to see if she was worthy.
Perhaps Madara fakes his death in the fanfiction after meeting Naruto. Naruto then has to deal with the chaos that follows as Madara secretly manipulates events from the shadows. Or, it could be that Naruto's presence causes Madara to have a change of heart, but then the ninja world doesn't believe that Madara has truly changed and they both have to fight against the world's distrust. There are so many ways the plot can take an unexpected turn in this kind of fanfiction.
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.
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 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.
In some fanfictions, there could be a plot twist where Madara and Naruto end up switching sides for a brief moment. Maybe Madara sees the error of his ways due to Naruto's unwavering belief in friendship and peace, and he helps Naruto defeat an oncoming threat, only to then go back to being the antagonist. Or perhaps Naruto discovers that he has a hidden connection to Madara's past, something that changes the whole dynamic of their battle and leads to Madara's defeat in a very unexpected way.
They could time travel to a future where everything they knew is in ruins. In this desolate future, they find out that their actions in the past led to this destruction. Now they have to work together to go back in time again and correct their mistakes. Sakura uses her intelligence to figure out what went wrong, while Madara uses his combat skills to protect them during their journey through time.