Another plot twist could be that Madara is being controlled by an even greater force when he captures Sakura. And Sakura realizes this and has to find a way to break the control on Madara while also escaping from him. This would completely change the direction of the story and introduce new challenges and opportunities for Sakura to show her strength and intelligence.
One possible plot twist could be that Sakura discovers a hidden weakness of Madara's during the fight. Maybe it's a chakra point that, when struck, temporarily paralyzes him, giving her an upper hand.
One possible plot twist could be that Sakura, during the time travel, accidentally alters the past in a way that instead of Madara becoming a villain, he becomes a hero. This change could completely shift the future she came from. For example, if she prevents Madara from finding certain power sources or meeting certain people who influenced his dark path, it could lead to a very different Naruto world. Maybe he would use his strength to unite the clans in a more peaceful way, and Sakura would then have to figure out how to return to her own time in this new timeline.
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.
Well, perhaps a plot twist could be that Sakura has a hidden Sharingan due to her relation to Madara. This would not only change her combat abilities but also her perception of the world. She might start to see things from an Uchiha perspective, which could lead to clashes with her friends. Another twist could be that Madara faked his death and comes back to recruit Sakura to his side, using their family bond as leverage. This would force Sakura to decide between her old life and a new path with her brother. Additionally, it could be that Sakura discovers some dark secrets about the Uchiha clan through Madara, which could put her in a difficult position in Konoha.
They could time travel to a future where everything they knew is in ruins. In this desolate future, they find out that their actions in the past led to this destruction. Now they have to work together to go back in time again and correct their mistakes. Sakura uses her intelligence to figure out what went wrong, while Madara uses his combat skills to protect them during their journey through time.
In such fanfiction, Sakura might be depicted as more alluring and perhaps more bold in her interactions with Madara. Madara could be shown as having a certain charm that draws Sakura to him.
Perhaps in the fanfiction, Madara kidnaps Sakura because he realizes her potential as a medic - nin. He wants her to heal his old wounds or maybe study her unique healing abilities to find a way to make himself invincible. He could keep her in a hidden lair and force her to perform medical experiments on him.
One possible plot twist could be that Naruto, after becoming a Madara fan, starts to question the traditional values of Konoha. He might see Madara's vision of a more unified world under his rule as something appealing. This could lead to a rift between him and his friends as they struggle to understand his new perspective.
Perhaps Madara fakes his death in the fanfiction after meeting Naruto. Naruto then has to deal with the chaos that follows as Madara secretly manipulates events from the shadows. Or, it could be that Naruto's presence causes Madara to have a change of heart, but then the ninja world doesn't believe that Madara has truly changed and they both have to fight against the world's distrust. There are so many ways the plot can take an unexpected turn in this kind of fanfiction.
Perhaps he sees her as a threat. Sakura is a skilled kunoichi, and Madara may want to prevent her from interfering in his plans. So he restrains her to keep her out of the way.