One idea could be that Shisui discovers a dark secret about Sakura's past that changes their relationship. Maybe she has a hidden power that she's been suppressing and Shisui helps her come to terms with it.
One plot idea could be that Shisui survives and he meets Sakura during a mission outside the village. He is intrigued by her medical skills and her strong will. They start to train together and a friendship forms that slowly turns into something more as they face various challenges together.
A plot could involve Sakura being targeted by an enemy who wants to use her medical knowledge for evil purposes. Shisui, being a skilled ninja, decides to protect her. As they go on the run together, they start to understand each other better. Shisui might teach Sakura some unique ninja techniques, and Sakura could help Shisui deal with his own emotional traumas. Another idea is that they both get involved in a mystery within the Hidden Leaf Village. There are strange disappearances, and they suspect that there is a powerful enemy at work. They have to use their combined skills, Sakura's intelligence and medical expertise and Shisui's combat and Sharingan abilities, to solve the mystery.
Another plot could involve them traveling to a time when their own clans were in a different state. For Sakura, she could see how the Haruno clan was more prominent in the past. Shisui could witness the Uchiha clan before all the unrest. They might get involved in family affairs and end up changing the future relationships within their clans in unexpected ways.
Perhaps there is a plot where an ancient curse is affecting the Uchiha clan, and Itachi and Shisui suspect Sakura might have some knowledge or power that could help them break it. They then team up with her to find a solution, and along the way, they discover new aspects of each other's personalities and abilities.
One plot idea could be that Itachi and Shisui are on a mission and they cross paths with Sakura. Shisui, being the friendly one, starts to teach Sakura some new jutsu skills. Itachi, initially reluctant, gradually warms up to Sakura's determination. Another could be a time - travel plot where Sakura goes back in time and meets a young Itachi and Shisui. She tries to prevent some of the tragedies that are to befall them in the future. And finally, a plot where Itachi and Shisui are in a life - or - death situation and Sakura, with her medical skills, has to save them and in the process, they form a strong bond.
One idea could be a time - travel plot. Sakura somehow gets sent back in time and meets Shisui. They form an unlikely alliance as Sakura tries to prevent certain tragedies from happening in the Uchiha clan. This would involve a lot of mystery and action as they work together, with Sakura using her medical ninjutsu knowledge and Shisui his Sharingan abilities.
There could also be other supporting characters. For instance, Naruto or Sasuke might make appearances in the fanfiction. Naruto could be a friend who offers his unwavering support to Sakura in her adventures with Shisui. Sasuke, as another Uchiha, might have some sort of connection or conflict related to Shisui's actions or decisions in the story.
One idea could be that Sakura, while on a mission with the Anbu team led by Itachi and Shisui, discovers a hidden jutsu that could change the balance of power in the ninja world. The Anbu team then has to protect her as she tries to master it and keep it from falling into the wrong hands.
One interesting Shisui Sakura fanfiction could be a story where they team up on a dangerous mission. Shisui's sharingan abilities combined with Sakura's medical and combat skills make them a formidable duo.
There could be various interesting stories. Maybe some focus on the characters' growth and development. For example, a character might start as a shy and weak individual but through a series of adventures in the fanfiction, they become strong and confident.