What if the time travel causes a split in the timeline? One where the original events still exist in a parallel universe, and the characters in the fanfiction are now in a new, uncharted version of their world. They then have to deal with the consequences of not only changing their own past but also the existence of a parallel, unchanged world.
Perhaps the person who initiates the time travel isn't who they seem. It could be an imposter who has their own motives for changing the past, like a Shadow in disguise. This would add a whole new layer of mystery and danger to the story.
Perhaps they travel forward in time instead. They could see the consequences of their actions in the future. Maybe they find out that their actions had unintended negative effects on some of their friends or the city as a whole. This would lead them to go back and try to fix things in a different way.
Maybe a ghoul travels forward in time and discovers that in the future, ghouls are no longer hunted because a new food source has been found. This would be a huge shock to the ghoul, who has only known a life of hiding and hunting humans. They could then try to bring this knowledge back to their own time to change things for the better.
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.
Well, a possible plot twist is that when they travel back in time, Sakura loses her medical skills. This forces her to learn them all over again in a more difficult environment in the past, and in the process, she discovers a new way of using medical ninjutsu that she brings back to the future. As for Kakashi, his Sharingan might behave differently in the past due to some temporal anomaly. This could lead to him having to control a new and unexpected power while also dealing with the enemies from that era. Also, they might find out that their time travel was actually set up by an enemy who wants to use their presence in the past to change the future to their advantage.
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 plot twist could be that the time - travel device they use was actually created by an ancient and forgotten wizard who had a hidden agenda. When Hermione and Lucius travel back, they discover that this wizard was trying to use them to change history for his own gain. They then have to race against time (literally) to stop this wizard from achieving his goal while also trying to return to their own time. This would add an extra layer of mystery and danger to their time - traveling escapade.
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.
A great plot twist could be that in the time travel, they end up in an alternate version of Hogwarts where the roles are reversed. Ginny is in Slytherin and Draco is in Gryffindor. This makes them see each other in a completely different light. They have to deal with the prejudices of their new houses while also trying to find a way back to their own time and original selves.
One interesting plot twist could be that when Merlin and Morgana time travel, they end up swapping their magical abilities. So Merlin has Morgana's dark magic skills and vice versa. This creates a whole new dynamic as they struggle to adapt to these new powers in a different time period.