Well, it could be a really cute story. Maybe Shisui and Sakura are in a cupcake shop and they see calla - shaped cupcakes. Shisui could be a bit of a prankster and try to steal a cupcake, while Sakura scolds him in a friendly way. And then they end up sharing a cupcake and having a great time.
In this fanfiction, it might be that Sakura is an expert baker and she makes special calla - flower - inspired cupcakes. Shisui comes by to taste them and he's so impressed that he wants to help her sell them. Along the way, they become closer friends and perhaps there's a hint of a deeper relationship developing. They could also use the calla and cupcake theme for a party or something.
One plotline could be that there's a cupcake - making competition in their village. Sakura enters, with Calla as her mascot. Shisui, who is initially just a spectator, gets roped into helping Sakura when she faces some difficulties. They create a cupcake that has calla - like decorations on it and end up winning the competition, much to everyone's surprise.
Another storyline could involve a dangerous situation on the train. Maybe there are bandits or some sort of enemy ninjas attacking the train. Shisui, being the powerful ninja he is, jumps into action. Sakura also uses her medical and combat skills to help. In the process, they form a bond of trust and friendship. After the incident, they continue to be friends and Sakura might even learn some new techniques from Shisui.
One possible plot could be that Itachi and Shisui are on a mission in the ANBU and they cross paths with Sakura who is also on a mission related to a medical emergency in a war - torn area. They initially have some misunderstandings as Sakura is not used to the ANBU's way of doing things, but eventually they work together. Itachi and Shisui use their combat skills while Sakura uses her medical ninjutsu to save a village from a hidden enemy's attack.
One possible plotline could be that Itachi and Shisui, being the skilled Uchiha they are, take Sakura under their wing to train her in some unique jutsu. Maybe they see her potential and want to help her reach a new level of power. For example, Shisui could teach her his body - flicker technique while Itachi imparts some of his knowledge about genjutsu. This would create an interesting dynamic as Sakura tries to adapt to their different teaching styles.
One possible plotline could be that Shisui, with his unique abilities, takes Sakura under his wing to train her in some special jutsu. Maybe he sees her potential that others haven't fully recognized. He could teach her how to better use her chakra control in a more unique way than Tsunade taught her.
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.
Well, one possibility could be that they are on a mission together. Sakura's medical skills could come in handy when Itachi or Shisui get injured. And they might face a powerful enemy that requires all of their skills combined to defeat. Maybe Itachi's Sharingan and Shisui's unique abilities, along with Sakura's strength and intelligence, make for an interesting dynamic.
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.
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.
It could be that Shisui has been acting secretively lately. Itachi, being observant, and Sakura, who is also perceptive in her own way, notice this. They glare at him because they suspect he might be involved in something that could put the village at risk. Maybe he has been meeting with some suspicious characters. Itachi and Sakura's glares are a way of showing that they are on to him and that he should come clean about what he's been doing. As the story unfolds, Shisui might reveal that he was actually trying to protect the village in his own way, but his methods were misunderstood by Itachi and Sakura, leading to a lot of drama and tension in the fanfiction.