Perhaps the fanfiction could focus on the little sister's own journey of self - discovery. Growing up in the shadow of her two powerful brothers, she might strive to find her own identity and power. She could train secretly and then surprise everyone with her newfound abilities. And in the process, Sasuke and Itachi might have to deal with their own feelings about their sister growing up and becoming independent.
Another plot could be that the little sister is in danger. Some powerful enemy might target her to get to Sasuke or Itachi. This forces the two brothers to put aside their differences and work together to protect her. Along the way, they might also learn more about their sister's strength and courage as she tries to fight alongside them despite being the youngest and seemingly the most vulnerable.
It could be a rogue ninja from their clan who has a vendetta against the Uchiha family in general. Since Sasuke and Itachi are already well - known, the antagonist might see the little sister as an easier target to get revenge on the Uchiha. He could try to kidnap her or harm her in some way.
In the fanfiction, Itachi might be acting according to some secret mission that endangers Sakura's life. Sasuke, who has a strong bond with Sakura now, won't let that happen. He jumps in and uses his ninja skills. Sasuke could have developed some new jutsu that he uses to counter Itachi's attacks. This not only saves Sakura but also shows Sasuke's growth as a ninja. And Sakura, in turn, might be in the middle of researching some important medical ninja stuff that Itachi's actions could have disrupted if not for Sasuke.
A plot could be that Sasuke's sister discovers a hidden power within herself that could either save or destroy the ninja world. Naruto and Sasuke have different views on how to handle this situation. Naruto wants to help her control it for good, while Sasuke is more cautious. This creates a conflict between them and also gives the sister a central role in the story, as she has to decide her own fate.
One interesting plot could be that Sasuke's sister has a unique power that both Naruto and Sasuke are unaware of. She could be a key to uniting the Hidden Leaf Village and the Uchiha clan in a new way. Maybe she has the power to heal the rift between the village and the remaining Uchihas after the massacre. And as Naruto and Sasuke are on their own paths of growth, she emerges as a bridge between them, helping them understand each other better.
One common theme is brotherly love. Itachi's love for Sasuke despite the hardships they face is often explored. For example, in many fanfictions, Itachi sacrifices a lot to protect Sasuke.
Love and friendship can also be themes. The sister might form deep friendships with other characters in the Naruto universe. And in some cases, there could be a romantic sub - plot for her. This could be with a character from her own clan or someone outside like a ninja from another village. These themes add different layers to the fanfiction and make it more engaging for readers.
It could be about Tenten's sister's adventures in the ninja world. Maybe she discovers a new jutsu or goes on a mission with Tenten and their friends.
The plot could start with Naruto growing up in the Uchiha clan as Sasuke's little brother. He might face discrimination due to being the Jinchuriki, but Sasuke would be protective. They could train together, with Sasuke teaching Naruto some of the Uchiha techniques. Later, when the clan is massacred, Sasuke might be even more determined to get revenge, and Naruto would be by his side, trying to stop him from going down a dark path.
Well, in the fanfiction, a likely plot development is that Naruto's newfound power, perhaps a unique form of Rasengan, is crucial in the fight against Itachi. Sasuke, on the other hand, is initially blinded by revenge but Naruto helps him see that there's more to Itachi's actions. This could lead to a situation where they don't actually kill Itachi but rather free him from whatever binds him to his 'evil' deeds. The fanfic might then explore how they deal with the consequences of not following through with the kill.
The plot could center around Sakura's role in Itachi's decision - making. Since she's his older sister, she has a certain influence over him. Maybe she has a different view on the Uchiha's situation compared to the elders in the clan. She could be the voice of reason for Itachi, guiding him to find a more peaceful solution to the clan's problems. For example, she could encourage Itachi to negotiate with the village leaders instead of following the orders blindly. And in the process, her relationship with Itachi would be explored deeply, showing their bond as siblings.