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.
Maybe in this fanfiction, there is a prophecy that a child born from a union between a certain shinobi (Kakashi) and a medic - nin (Sakura) will bring great change to the ninja world. So, some forces manipulate events to make Sakura pregnant. Kakashi and Sakura then have to figure out the truth behind this while also preparing for the arrival of their baby. They might face many challenges, like dealing with the political implications within the village, as well as the moral and ethical questions that come with such a manipulated situation.
One possible plot twist could be that the pregnancy is not as straightforward as it seems. Maybe there are some hidden powers or curses involved that are affecting the pregnancy. For example, the unborn child could have a special chakra that is attracting enemies.
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.
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.
One plot idea could be that they are facing unexpected pregnancy during a time of great unrest in the ninja world. They have to balance their duties as ninjas and their new roles as parents - to - be. Shikamaru might use his intelligence to plan for their future and Sakura would use her medical skills to ensure a healthy pregnancy.
Perhaps Sakura was being too overconfident and reckless in a battle situation, which put her teammates at risk. Kakashi, as her sensei, decides to punish her. He could make her practice teamwork exercises alone for a while, where she has to simulate different battle scenarios with puppets or something similar to learn how to better cooperate with others.
Well, perhaps in the fanfiction, Sakura discovers she has a baby from some sort of mysterious experiment gone wrong. Kakashi, being the reliable and kind - hearted ninja he is, steps in to help her. He teaches her how to be a strong mother while also protecting the baby from those who might want to use it for their own evil purposes. They end up forming a little family unit of sorts.
In this kind of fanfiction, perhaps Kakashi notices Sakura's potential that is being overlooked. He might start training her more intensively, leading to Sakura developing new jutsu skills. For example, Kakashi could teach her some of his own special techniques, like his lightning - style jutsu in a modified form suitable for Sakura.
One possible plot could be that after years of fighting side by side and growing closer, Kakashi finally realizes his deep feelings for Sakura. They start dating secretly at first, not wanting to disrupt the village's harmony. Then, as their relationship blossoms, they decide to get married. Their wedding could be a grand event in the village, with all their friends and comrades coming to celebrate. It could also show how they face challenges together as a married couple, like dealing with new threats to the village while also maintaining their relationship.
One possible plot twist could be that it's all a dream of Sakura's. Maybe she has a deep - seated longing for Kakashi, but she's been suppressing it. And the kiss in the fanfiction is her subconscious mind's way of expressing that hidden desire.