One interesting plot twist could be Naruto changing the past in a way that completely alters the future relationships. For example, if he manages to prevent certain tragedies from happening to his friends' families, it could lead to very different dynamics. Maybe Sasuke's family wouldn't be massacred, and Sasuke would grow up in a completely different environment, which might change his entire attitude towards the village and Naruto himself. This could lead to a whole new set of adventures and challenges for Naruto as he tries to adapt to this new timeline.
A possible plot twist is that Naruto's time travel affects his own powers. He could find that in the past, his chakra has different properties or that he has access to new jutsu that were lost in his time. This could make him a much more powerful and unpredictable force. On the other hand, it could also attract unwanted attention from those in the past who might see his new abilities as a threat. This would create a situation where Naruto has to balance using his new powers to fix things while also avoiding being hunted down by those who fear him.
Perhaps Naruto travels back and discovers that the origin of the ninja world's problems is something completely different than what he thought. He might find out that there was a more sinister force at work from the very beginning that was manipulating events. This could lead to him having to form new alliances and fight against enemies that he never knew existed in his original timeline. It could also change his perception of the older generation of ninja who might have been unknowingly influenced by this hidden force.
One possible plot twist could be Naruto changing the past in a way that completely alters the future relationships. For example, if he prevents a certain event that led to a character's death, it could change the whole dynamic among the characters. Another twist could be that Naruto discovers that the past is not as simple as he thought, and there are hidden forces at work that he didn't know about in his original timeline.
One possible plot twist could be that Naruto and Jiraiya travel back to a time when the Uchiha clan was at its peak. This would put Naruto in a position to potentially prevent the Uchiha massacre. He could use his knowledge of future events and his skills to change the course of history for the better. Jiraiya, on the other hand, could discover secrets about the Uchiha that were lost over time.
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.
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.
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.
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.
A really cool plot twist would be if during their time travel, they find out that time itself is a sentient being or is being controlled by an unknown force. This force has been manipulating events in the Soul Society and the human world all along. Ichigo and Urahara then have to figure out how to deal with this new discovery, whether to fight it or try to negotiate, while also trying to find their way back to their own time.
A cool plot twist could be that when they travel back, they find out that someone else from the future has also come back and is actually causing more chaos. Maybe it's a villain who wants to change the past in a way that benefits them even more than Orochimaru's original plan. Another twist could be that Naruto and Gaara accidentally change something that has a much bigger impact on the future than they expected, like causing a different person to become Hokage.
One exciting plot twist could be a character from the Naruto universe who travels back in time to the Jedi universe and discovers they are actually a long - lost Jedi descendant. This completely changes their understanding of their own powers and heritage.
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.