A possible plot twist is that Sakura's kidnapping is a test. It could be a test set by an ancient ninja clan to see if she is worthy of some great power or knowledge. Sasuke, who is involved in this in a mysterious way, might be there to either help or hinder her depending on her actions during the kidnapping. This could lead to a complete change in their relationship as they face this strange situation together.
Well, perhaps the kidnapping is part of a larger scheme to lure Naruto into a trap. Since Sasuke and Sakura have a connection to Naruto. Or it could be that the kidnapper Sasuke is actually under a mind - control spell, and Sakura has to find a way to break it to save both of them. Maybe she uses her medical skills in an unexpected way to do so.
One possible plot twist could be that Sasuke is not the real kidnapper. Maybe he has an evil clone or someone is framing him. Another could be that Sakura has a hidden power that she discovers during the kidnapping ordeal, which changes the power dynamic. For example, she might be able to communicate with a spirit that helps her escape.
A really unexpected plot twist could be that the kidnappers are actually the good guys in a convoluted way. Maybe they know of a prophecy that Sasuke and Sakura are fated to bring destruction, so they are trying to stop it. Another idea is that during the kidnapping, Sasuke and Sakura end up in a different dimension where they have to rely on each other in completely new ways. Plus, the motives of the kidnappers could be related to a secret that Sakura has been hiding about her family all along.
One possible plot twist could be that the kidnappers are actually being controlled by an old enemy of Naruto's village who wants to use him as a bargaining chip to get some ancient scrolls. Another could be that Naruto is kidnapped by someone who thinks he is the key to a powerful jutsu they want to unlock, but in reality, they have the wrong idea about Naruto's abilities. Maybe the kidnappers are from a hidden group within the ninja world that has a grudge against the Uzumaki clan and Naruto specifically.
Well, perhaps in the fanfiction, Sakura is kidnapped by Sasuke because he wants to use her as a bargaining chip against Konoha. Then, the story could involve the other Konoha ninjas coming together to strategize a rescue mission. They might have to deal with Sasuke's new and powerful abilities that he has acquired during his time away. Sakura, while kidnapped, could also try to talk some sense into Sasuke, appealing to their past friendship and her feelings for him.
One possible plot twist could be that the pregnancy is a result of some sort of ancient jutsu gone wrong. Maybe a forbidden technique that was meant to save Madara's life but instead had the side effect of causing Sakura to become pregnant. Another could be that an enemy has somehow manipulated their DNA to create the pregnancy as part of a grand scheme to control the two powerful shinobi.
One possible plot twist could be that right before the wedding, Naruto has to go on a dangerous mission. This could put their relationship to the test as Sakura has to deal with the fear of losing him. She might even consider calling off the wedding. Another plot twist could be that an old enemy resurfaces and tries to use Sakura as a leverage against Naruto, forcing him to make a difficult choice between his love and the safety of the village.
A plot twist could be that their deaths were faked by themselves. They might have discovered a great threat to the village that required them to go undercover. So, they faked their deaths to deceive the enemy. Or, perhaps their deaths lead to the awakening of an ancient evil that was sealed long ago. And it turns out that their deaths were somehow a sacrifice to keep this evil at bay for a while, but now the remaining characters have to find a way to defeat it once and for all. This would completely change the direction of the fanfiction.
One possible reason could be that Sasuke's past traumas and his continuous search for redemption make him feel unworthy of Sakura's love. He might think he's dragging her down and decide to end the marriage for her own good.
The curse mark could have a mind of its own. It starts to communicate with Naruto and Sasuke in their dreams, trying to manipulate them into doing its bidding. Naruto, being the optimistic one, tries to resist and turn the curse mark's power into something positive. Sasuke, however, is more tempted by the power it offers. This could lead to a rift between them as they have different approaches to dealing with the curse mark, and their relationship would be put to the test.
One possible plot twist could be that they face opposition from their respective clans who still hold grudges from the past. The Uchiha clan might not accept Naruto easily due to his connection to the Nine - Tails. Another twist could be that Sasuke discovers a new power within herself during their marriage that has unforeseen consequences for the village. Maybe it attracts enemies who want to steal that power.
One possible plot twist could be that Naruto, upon getting Sasuke's Rinnegan, starts to see visions of the past and future of the Uchiha clan. This new power might make him question his own beliefs and the relationship between the Senju and Uchiha. He could see the events that led to Sasuke's decision to give him the Rinnegan and struggle with the responsibility that comes with this powerful dojutsu.