One interesting plot could be that Sakura discovers a hidden power within herself that is somehow connected to Shisui's Sharingan. Maybe it's a power that can only be unlocked when they are in close proximity to each other. They initially don't understand this connection but as they train together, they start to figure it out. This could lead to them having to face a powerful foe who is after this unique power. Another plot could be that Shisui fakes his death for some reason and Sakura is one of the few who suspect that he is still alive. She goes on a quest to find him, and when she does, they have to work together to clear his name and expose the real villains in the shinobi world.
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.
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.
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.
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 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.
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.
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 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.
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.
One plot idea could be a story where a young ninja discovers they have received Shisui's eyes through some mysterious means. They then have to learn to control the unique powers of the eyes, like the powerful genjutsu abilities. This could lead to them being hunted by those who want to use the eyes for evil purposes.
Another interesting aspect is their potential as comrades. Fanfictions may show them teaming up on missions. Since Shisui has his unique Sharingan abilities and Sakura has her medical and combat skills, they could make a formidable team. They might have to rely on each other's strengths to overcome various challenges during the mission, which can create some exciting storylines.