One interesting plot twist is if they time travel and find that the world they end up in has a different version of the Chakra system. They have to adapt quickly to this new form of energy while also trying to find a way back home. Also, imagine if they time travel and discover that Naruto was supposed to be born in a different village in this alternate timeline. This would completely change the way they view Naruto's destiny and their role in protecting him.
Well, a frequent plot twist is when the time travel affects the relationships within Team Minato. Maybe they go back in time and realize they were wrong about someone. Or they accidentally change something in the past that makes one of their relationships turn sour. Also, they could find out that someone they thought was an enemy in their original time was actually a friend in the past, which is a huge revelation and changes the whole dynamic of the story.
Well, perhaps a plot twist is that when they time travel, they end up switching bodies. Naruto, in Minato's body, has to deal with the responsibilities of being a Hokage in the past, while Minato, in Naruto's body, has to navigate through Naruto's life in the present. This would create a lot of comical and also very tense situations as they both try to adapt and not mess up the timeline.
A cool plot idea could be Minato traveling back to his own childhood. He could then use his future knowledge to train himself more effectively, making himself an even more powerful shinobi at a younger age. This would have a huge impact on the future of the Leaf Village as he would be able to better protect it earlier. He might also be able to prevent some of the early tragedies that happened in the village.
A really cool plot might be that Kakashi time travels and discovers a hidden conspiracy in the past that was related to Team Minato. He then has to work with his past comrades, including Minato, to uncover the truth and prevent a great disaster that he knew about from his own time.
One interesting plot twist could be that Minato travels back to a time when the Hidden Leaf Village is on the verge of a civil war. He uses his future knowledge to prevent it, changing the entire future of the village. Another could be that he travels to a time where his parents are still alive and has to deal with the complex emotions of seeing them again.
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.