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.
One interesting plot twist could be that Thor goes back in time and accidentally changes something that makes him lose his powers. For example, he might prevent the event that led to him getting Mjolnir, and then has to find a new way to be a hero without his trusty hammer. Another could be that he goes back and meets a younger version of Loki who doesn't yet hate him, and he has to figure out how to keep it that way so that their relationship in the future is different.
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.
Maybe he goes back in time and meets a younger version of his enemy. Instead of fighting right away, he tries to understand what made the enemy turn bad in the first place. This changes the whole future dynamic between them when he returns to his own time. He might find out that there was a misunderstanding that led to all the hatred.
One interesting plot twist could be that when Lucy goes back in time, she discovers that her family has a much darker secret than she ever knew. Maybe they were involved in some sort of magic that was considered forbidden in the past. Another could be that she accidentally changes the future in a way she didn't expect, like making her friends not become the people she knew them as. And perhaps she finds out that an enemy in the present was actually once an ally in the past, and she has to figure out what went wrong to turn them into an enemy.
A cool plot twist might be that Fem Harry goes back in time and discovers that her parents were involved in a secret mission that was never revealed before. This could lead to her having to deal with the consequences of uncovering that truth. Also, she could find out that Voldemort had a different origin or a hidden weakness that was lost in history. As she tries to use this knowledge to defeat him earlier, she might face opposition from some of the older wizards who don't believe her or are afraid of the changes she could bring. It could also be that she changes the way magic is taught at Hogwarts, introducing new spells or techniques from the future that create a whole new set of challenges and opportunities for the students.
A possible plot twist is that Kakashi goes back in time and finds out that the events he thought were true in the past were actually misinformation. This could completely change his perception of the history of the ninja world and his own role in it. Also, he might go back to a time when Orochimaru was just starting his dark experiments. Kakashi could try to stop Orochimaru right from the start, but in doing so, he might end up creating new villains or problems. Or perhaps, when he travels back, he loses some of his memories from the future, which makes it difficult for him to use his knowledge effectively to change things.
One common plot twist could be that Naruko discovers she has the power to change not only her own fate but also the fate of the entire village. For example, she might prevent a major disaster that originally happened in the past. Another could be that she finds out a hidden truth about her family or a powerful jutsu that was lost in time. Maybe she realizes that a person she thought was an enemy in the present was actually a friend in the past and has to figure out how to reconcile that in the future.
Well, sometimes in these fanfictions, a plot twist might be that Sirius goes back in time and discovers a hidden truth about his family. Maybe he finds out that there was a secret alliance or a hidden enemy within the Black family that was influencing events all along. This could completely change his perception of his family's past and his place in it. Also, he could go back in time and end up being involved in a different kind of magic that was lost in his original time, like an ancient form of magic that has the power to either save or destroy the wizarding world.
One possible plot twist could be that when they go back in time, they accidentally change something that has a huge impact on their future relationships. For example, Naruto might unknowingly prevent Sasuke from leaving the village in the past, which could completely change how they interact in the present they return to. Another could be that they find out a hidden truth about their parents or the village's past that was covered up, like a secret alliance that their predecessors were involved in.
Imagine a fanfiction where Sakura, instead of being in love with Sasuke, has feelings for Naruto all along. This would completely change the love triangle aspect and lead to a lot of interesting interactions between the three main characters. It could also cause Sasuke to re - evaluate his relationship with his teammates.