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 Ginny and Draco's pregnancy is a result of a magical accident. Maybe a spell gone wrong during a battle or an experiment that binds their magical essences together. Another could be that they keep the pregnancy a secret from everyone at first, and as they struggle to come to terms with it, they start to develop unexpected feelings for each other. For example, Draco, who has always been a bit of a snob, realizes Ginny's true strength and kindness through this situation. And Ginny sees a more vulnerable side of Draco that she didn't expect.
One interesting plot twist could be that Draco and Ginny initially resist the arranged marriage but then find common ground in their shared love for a particular magical art, like potions. They start working together secretly on new potion recipes and gradually fall in love. Another twist could be that there is a mystery surrounding the arranged marriage, like it was actually set up by an enemy to cause chaos in the wizarding world. As they dig deeper, they uncover a conspiracy and have to work together to stop it. And a third plot twist might be that Ginny discovers she has a long - lost relative who is related to Draco's family, which changes their perspective on the arranged marriage completely.
Well, perhaps they time travel to a moment before they were even born. There, they discover a hidden prophecy that has to do with their soul bond. This prophecy might say that their bond is the key to saving the wizarding world from a future threat that no one else is aware of yet. So, they have to figure out how to fulfill this prophecy while also dealing with the challenges of time travel and keeping their bond intact.
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.
One possible plot twist could be that Draco's family objects strongly to the marriage. His pure - blood supremacist parents might see Ginny, a Weasley, as beneath them. They could try to sabotage the relationship, which would create a lot of drama. Maybe they'd spread false rumors about Ginny in the wizarding community.
One idea could be that their children inherit a mix of their magical abilities. For example, having Draco's skill in potions combined with Ginny's talent for charm work. Another plot could involve their children facing a new dark threat at Hogwarts and having to use their unique family heritage to fight it. Maybe they have to deal with a new type of dark magic that is a combination of old pure - blood magic and some forgotten spells.
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.