Sasuke might regret it if he later finds out that Fem Naruto was the key to achieving true peace in their world. Maybe she had a unique ability or knowledge that could have united the warring factions, and by killing her, he doomed their world to more conflict and chaos.
Another reason could be guilt. If Sasuke was manipulated into killing Fem Naruto by an outside force and later discovers the truth, he would feel an intense sense of guilt and regret for being used to end her life.
In some fanfictions, Sasuke might regret killing Fem Naruto due to a realization of their shared past. Maybe he finally understands the bond they had that was broken by his actions. It could also be that he discovers new information about her that makes him see his act as a huge mistake.
Another character could be Kakashi. Maybe he has to make a tough decision that goes against Fem Naruto's wishes. For example, not allowing her to go on a dangerous mission she really wants to. This could make Fem Naruto feel betrayed and heartbroken, as Kakashi is a respected figure in her life.
Perhaps Fem Sasuke in this fanfiction has a different view of the world. She might believe that Naruto is a threat to her goals or to the future of the ninja world she envisions. It could also be that she has some deep - seated emotional pain that she blames Naruto for, and that leads her to kill him.
Well, perhaps in the fanfiction, Fem Sasuke's blindness is a result of some dark jutsu. Naruto, with his determination, tries to find a way to restore her sight. Along the way, they encounter many old foes and new allies. The story could explore how Fem Sasuke copes with her new disability and how it changes her ninja skills, for example, she might develop new ways of using her Sharingan even without sight.
It could also be due to a power struggle. Fem Sasuke might be jealous of Naruto's growing power and influence. In some fanfictions, characters can be driven by envy, and she might see Naruto as a rival that needs to be put in her place, so she ends up hurting him.
The plot might involve Naruto with the Rinnegan being a bit of an outcast in the village at first because of the strange and powerful new dojutsu. Fem Sasuke could be the one to understand him and encourage him to embrace it. They could then go on a quest to discover the origins of the Rinnegan together, facing various challenges along the way, like ancient ninja traps and powerful, long - forgotten clans.
One possible plot could be that Sasuke realizes his deep connection with Fem Naruto over time. Maybe they go on various missions together and he starts to see her in a new light. As they face challenges side by side, his feelings grow into love and he decides he wants to marry her. He then has to overcome the initial shock of the village and their friends, as it's an unexpected pairing.
The plot could involve them starting a family. Fem Sasuke might be hesitant at first, worried about passing on her troubled family history. However, Naruto is excited and encourages her. They could have a child who has a unique combination of their powers. And then they have to protect this child from various threats, both from outside the village like rogue ninjas who might want to kidnap the child for its power, and from within the village where some might be jealous or fearful of the child's potential. This would bring them closer together as they work as a team to keep their family safe.
One possible plot could be that in this fanfiction, Sasuke finds a female Naruto in a weakened or some special state and decides to take her in as a pet. Maybe Naruto has lost her memories and Sasuke, out of some complex feelings like protectiveness or curiosity, keeps her around. He might train her like a pet at first, but as time goes on, their relationship could start to change and develop into something more complex and deep.
One common theme is friendship. Since Naruto and Sasuke's relationship is so central in the original series, in fem versions, their friendship or evolving bond is often explored. Another theme is rivalry, but with a different female - centered dynamic. For example, how they compete in a world that might have different expectations for female ninjas.