Maybe the memories weren't really removed but rather hidden in a way that only a certain powerful magic can unlock. And when they start to surface, they bring with them a dark secret that could change everything. It could be related to an evil entity that was using Hermione's time - travel for its own gain.
A possible plot twist could be that the person who removed her memories was actually her future self trying to protect the timeline. This would add a whole new layer of complexity to the story.
One great fanfic on this topic is 'Time's Erasure'. It delves deep into how Hermione copes without those memories and how it impacts her relationships. The author does an amazing job of showing her confusion and the slow realization that something is amiss.
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.
One plot twist could be that her secret father is actually an enemy in disguise. He might have some evil plan that involves Hermione unknowingly.
One possible plot twist could be that Draco's family initially opposes the marriage. His pure - blood - supremacist parents might have a hard time accepting Hermione, a Muggle - born. Another twist could be that there are dark forces at play trying to use their union for some evil purpose, perhaps related to an ancient prophecy. And a third twist could be that Hermione discovers a long - lost family secret that has some connection to the Malfoy family, which changes the dynamics of their relationship and the marriage.
Perhaps they time travel to a period when a great evil was first emerging. They then have to figure out a way to stop this evil from taking root without using the knowledge and power they have in their own time. This could involve finding and training local ninja in the past to fight against this new threat, and in the process, they learn new techniques and strategies that they can bring back to their own time.
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.
One possible plot twist could be that Ichigo travels back in time and accidentally changes something that makes him not become a Soul Reaper in the first place. This would completely change his destiny and the future of the Soul Society. Another could be that he travels to a time when an ancient evil was first sealed away, and his presence there somehow weakens the seal, leading to a new threat emerging in his present time.
One possible plot twist could be that when they time travel, they accidentally change a key event in the past that has a domino effect on their present. For example, they might prevent the formation of a guild that was crucial in their original timeline. Another could be that they find out they are related in some unexpected way through their time - traveling adventures. Maybe Ultear discovers she has a connection to Natsu's family that was lost in history. Or perhaps they time travel to a future where everything they know is in ruins, and they have to figure out how to prevent it in their present.
One possible plot twist could be that when they travel back in time, they accidentally change a small event that has huge consequences in the future. For example, they might prevent a key meeting between two clans, which then alters the political landscape of the ninja world. Another could be that they find out that one of them was actually from that time originally and had their memories wiped in the future. This would completely change their understanding of themselves and their place in the ninja world.
A possible plot twist could be that the time travel was all a simulation created by an enemy to deceive the main character. So, the character thinks they are changing the past or future but are actually being manipulated within a false reality.