One possible plot twist could be that their time travel messes up the existing timeline in ways they didn't expect. For example, they might accidentally prevent important events from happening in the past that were crucial for the future they came from. Another could be that they find out they were meant to time travel all along to fix a long - hidden problem in the ninja world's history.
Well, perhaps a plot twist could be that they time travel to a future instead of a past. And in this future, the ninja world is in ruins because of a decision they made in their original time. It would be a shock for them to see the consequences of their actions in such a drastic way. Also, they could discover that a character they thought was an enemy in their time is actually a hero in this future.
In Juubi Naruto time travel fanfiction, plot twists can be really exciting. For instance, Naruto might find out that the Juubi has a different origin in the past than what he thought. This could completely change his perception of the tailed beasts and his role as the Jinchuriki. It could lead to him having to form new alliances or fight new enemies in the past.
One possible plot twist could be that Naruto and Tayuya travel back to a time when the Hidden Leaf Village was first founded. This would put them in the middle of the early power struggles and they might have to use their future knowledge to prevent a great disaster. For example, they could stop a rogue ninja from stealing important village secrets that could have changed the course of the village's history.
In some fanfictions, a plot twist could be that Naruto and Yugito are the only ones who can see a strange and dangerous phenomenon. Everyone else in the village thinks they are crazy. They have to prove that this phenomenon is real and find a way to stop it from destroying the village. This makes them an unlikely duo against a mysterious threat that no one else believes in.
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.
Well, one plot twist could be that fem Naruto, due to her different personality as a female, might form alliances in different ways during the time travel. For example, she could use her charm to get closer to some characters that male Naruto might not have. Shikamaru, on the other hand, might use his intelligence in new ways. Maybe he figures out how to change the future in a more subtle way that no one expects. Another twist could be that their relationship changes. In the original, they were friends, but during time travel, they could become something more, like romantic partners, which would completely change the dynamics of the story.
A really interesting plot twist in some fanfictions is that Naruto's time travel with the Rinnegan actually creates an alternate timeline. This means that the future he came from may no longer exist, and he has to deal with the new reality he's created. It often leads to complex storylines where Naruto has to decide whether to try and restore the original timeline or embrace the new one.
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.
One possible plot twist could be that when they travel back in time, they accidentally change a crucial event that alters the future in unexpected ways. For example, if they prevent a key battle from happening, it might lead to a different power structure in the ninja world.
Maybe Naruto travels back to his own childhood days. He could use his knowledge as Hokage to help his younger self become stronger faster. He might also be able to prevent some of the hardships he faced, like not having enough food sometimes. This would not only change his own life but also the relationships he had with people like Iruka - sensei, who took him under his wing when he was a lonely kid.
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.