Well, a plot twist might be that the pregnancy is part of a prophecy. In the fanfiction world, it could be foretold that a child born to Shisui and Sakura would have some extraordinary power that could either save or destroy the ninja world. This would put them in a very difficult situation as they would be constantly in danger from those who want to either protect or prevent the birth of the child. Also, perhaps Sakura discovers she has a rare medical condition during the pregnancy that only she can have because of her unique chakra nature, and it adds a whole new layer of drama.
One possible plot twist could be that the pregnancy is a result of some sort of experimental jutsu gone wrong. Maybe they were trying to save someone and the jutsu had an unexpected side effect on Sakura. Another twist could be that there is some mystery behind who the father really is, even though it seems to be Shisui at first. There could be an enemy who has the ability to manipulate memories and create false impressions of events.
Another plot twist could be related to the origin of the pregnancy. Maybe there's some sort of magic or experiment involved that causes Sakura and Sai to become pregnant in an unexpected way. This could lead to a lot of self - discovery for the characters as they deal with this unforeseen situation.
A really interesting plot twist could be that Shisui and Itachi find out that Sakura has a connection to an ancient and powerful clan that they didn't know about before. This connection could bring in new elements to the training, like special techniques or a deeper understanding of the ninja world that they have to incorporate into her training.
One possible plot twist could be that Naruto inherits some of Shisui's unique abilities. Since Shisui was known for his powerful Sharingan techniques, Naruto might develop a new form of jutsu that combines his own chakra control with the Sharingan - like skills he could potentially inherit. This would make him an even more formidable ninja in the story.
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.
Perhaps the plot twist is that Shisui faked his death not just to protect the village in the general sense, but specifically to keep Naruto safe. He knew of Naruto's importance as the Jinchuriki of the Nine - Tails and his relation to Naruto as a brother. So, he went into hiding and has been secretly guiding Naruto from the shadows all along. This would add a whole new layer to Naruto's journey and the events that have unfolded in the series so far.
One possible plot twist could be that Lorelai initially tries to hide her pregnancy from her family and friends. She might be afraid of their reactions, especially if she's not in a stable situation. For example, if she's a young woman still in school or just starting out in her career, the pregnancy could be a huge disruption.
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 in the fanfiction, there's a mission where they are the only survivors and during their time of isolation, they develop a deep bond which leads to Sakura getting pregnant. The story could then revolve around how they deal with this new situation, with Kakashi trying to protect Sakura and the unborn child from any potential threats.
One possible plot could be that they are in a world where enemies have become allies. Madara, with his powerful abilities, and Sakura, with her medical skills and strength, find themselves in a situation where they accidentally get closer and Sakura becomes pregnant. This could lead to a story of them trying to protect their unborn child from various threats in the shinobi world while also dealing with the shock and change in their relationship.
Well, the plot could involve a time - travel element. Sakura somehow gets sent back in time and meets a young Shisui. At first, Shisui is suspicious of her, but as Sakura shows her skills and kind nature, he starts to fall for her. Meanwhile, Sakura is also drawn to Shisui's charisma and his strong sense of justice. As they navigate this strange situation together, their love story unfolds. They have to deal with the knowledge that Sakura doesn't belong in this time period, but their love is so strong that they try to find a way to be together regardless.