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.
Perhaps there could be a rival who tries to break them apart. This rival could be someone from Sasuke's past who has a grudge against him and sees Sakura as a way to get revenge. They might spread false rumors about Sasuke to make Sakura question his loyalty.
One possible plot twist could be that Itachi has been mind - controlled to kidnap Sakura. Maybe an enemy of Konoha has a powerful jutsu that forces Itachi to do this against his will. Another twist could be that Itachi kidnaps Sakura as a means to protect her from a greater threat in the shinobi world that no one else is aware of yet. He might know that she has some sort of power or knowledge that makes her a target, and by kidnapping her, he can keep her safe in a hidden location.
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 Sasuke was actually being controlled by an unknown enemy when he kidnapped Hinata. This enemy might be using Sasuke's power to get to Naruto through Hinata. Another twist could be that Hinata has some hidden power or knowledge that Sasuke's side needs, and the kidnapping is a way to extract that from her. Maybe it turns out that Hinata was expecting the kidnapping all along as part of a larger plan to infiltrate Sasuke's group and learn their true intentions.
Another plot twist could be related to the pregnancy itself. What if Sakura's pregnancy was not a natural one but rather the result of some kind of experiment or curse? This could lead to a whole adventure where she has to find a way to break the curse and save her unborn child. She might have to team up with unlikely allies and face powerful enemies in the process.
In a fanfiction like this, they could be on a diplomatic mission to another village. After the official business is done, they are invited to a banquet where they get drunk. While drunk, Sasuke might get into a friendly argument with Sakura about different fighting techniques. Sakura, being tipsy, could be more assertive in her views. This could lead to them sparring drunk (in a harmless way) and then realizing how much they enjoy each other's company even when not in a serious ninja - related situation.
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 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.
One possible plot twist could be that Sakura discovers Kakashi has a secret past she never knew about. Maybe he was involved in some kind of dangerous mission long ago that has consequences in the present. This could put a strain on their relationship as she tries to come to terms with this new information.
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.