A possible plot twist could be that when they travel back, they find out that the past is not as they remembered it. Maybe some events were actually caused by an unknown enemy manipulating things from the shadows all along.
One really interesting plot twist could be that the time travel was actually a trap set by a powerful villain. When Team 7 and Kakashi go back in time, they unknowingly set in motion a series of events that will lead to the villain's rise to power in their original time. They then have to figure out how to stop this while also dealing with the challenges of the past.
Another plot twist could be related to Kakashi's own abilities. Since he has knowledge of the future, he might try to use some jutsu or skills that he hasn't learned yet in his original time. But this could come with a cost, like draining his chakra too much or attracting unwanted attention from powerful enemies. He could also accidentally teach his past self some skills that change the course of his own development.
There's also 'Back to the Beginning: Team 7's Time Travel'. Here, Team 7 travels back to a crucial point in the Naruto universe's history. They end up changing some small things which have big consequences later. It's full of action and the character development is really well - done.
A great plot twist could be that Darth Vader travels back to the time when the Jedi Order was at its peak. His dark side presence is detected by the Jedi Council immediately. However, instead of being able to simply capture or kill him, they find that his knowledge of future events gives him an edge. He might use this to manipulate the Jedi, creating internal strife within the Order. This could also lead to some Jedi being tempted by the dark side because of the power that Vader represents. And all of this could ultimately reshape the future of the galaxy far more than anyone expected.
Maybe Team 7 travels back in time to a period when a powerful and evil force first emerged. They then try to stop this force from growing in the first place. Along the way, they face challenges like not being recognized by the people of that time, and having to adapt to the older ways of doing things in the ninja world. They might also encounter versions of their own families or friends in the past and have to deal with the emotional turmoil of seeing them but not being able to fully interact as they are from different times.
One interesting plot twist could be that Naruto, with his knowledge of the future, tries to prevent certain tragedies but ends up causing new ones. For example, he might try to save a character too early and disrupt the natural flow of events, leading to unforeseen consequences.
Perhaps the writer goes back in time thinking they can use their knowledge of the future to their advantage, but instead they find that the past has its own rules and forces that prevent them from doing so. For instance, every time they try to introduce a future concept, it gets distorted or erased by some mysterious force, adding a sense of mystery and frustration to the story.
A possible plot twist could be that one member of Team Hebi, say Karin, is actually from the future and has been manipulating the time - travel events all along to achieve a certain goal, like saving her own clan. This would completely change the team's dynamic and their perception of her.
Another great Kakashi back in time fanfiction idea is him going back to the time right before Obito's 'death'. He could then change the events that led to Obito's fall to the dark side. This would rewrite the entire future for the Ninja world, as Obito played such a crucial role in many of the later events, including the Fourth Ninja War.
A common plot twist is that Kakashi is secretly related to the 9 - Tailed Fox in some way. Maybe his family had a hidden pact with the fox's power long ago.
One possible plot twist could be that Naruto, when he travels back to graduation, realizes he has some of his future skills and knowledge. He might use this to outperform everyone in the exams in unexpected ways, like using advanced jutsu that no one has seen before, which would shock his classmates and teachers.