Perhaps the story could start with Shirou's transformation into a girl as part of a grander scheme by an unknown enemy. As a girl, he has to infiltrate a female - only society or event to gather information. This would force him to adapt quickly to his new identity. He would have to learn how to act like a girl, from his mannerisms to his speech. And during this process, he might develop new relationships and face challenges that he never would have in his male form, all while trying to figure out who is behind this transformation and stop their evil plans.
Well, one possible plot could be that Shirou wakes up one day as a girl and has to deal with all the new physical and social changes. His friends might be really confused at first, like Saber who would be very surprised to see her master in a different form. Shirou, now as a girl, might struggle with things like wearing dresses and having different hormonal emotions. And he would have to face enemies in this new form too, which could lead to some really interesting battle scenes where his opponents underestimate him because he's now a girl.
Saber would probably be quite shocked at first. She's used to Shirou as a male, and this sudden change would make her re - evaluate their relationship. Rin might be more intrigued and try to figure out what caused the transformation. Archer would likely be a bit dismissive at first, but then realize that Shirou in this new form still has the same determination. Illya might find it really funny and tease Shirou a lot about it.
A plot could involve Shirou being transferred to the Highschool DxD school. He quickly catches the attention of Rias and her peerage. His different style of combat and his unwavering determination might lead to some friendly rivalries within the group. He could also introduce some new concepts of magic that the DxD characters have never seen before, like his ability to reinforce objects. And he may find himself in the middle of the power struggles between the different factions in this new world.
A plot possibility could be that Shirou has to keep his transformation a secret at first. He's afraid of how others will react, especially those he cares about. So he tries to act as normal as possible while dealing with the physical and emotional changes privately. Another could be that some sort of magic gone wrong caused the transformation, and he has to find a way to reverse it while also using his new form to his advantage in battles or other situations.
One possibility is that his relationships with other characters would change drastically. For example, his interactions with Saber might become more complex, perhaps evolving from a more traditional male - female dynamic to a more nuanced friendship or rivalry. His friends like Rin might also be very surprised at first but then gradually accept this new version of him. And in battles, his fighting style might be affected as well, since his physical form is different now.
One possible plot could be them adjusting to married life in a world filled with the challenges and magic from their respective backgrounds. Maybe they have to face enemies together who are against their union, and they rely on each other's unique skills to survive.
Perhaps Shirou becomes an Avenger due to a misinterpretation of his ideals. He always wanted to be a hero who saved everyone, but in a world where his actions are constantly misconstrued and lead to more harm than good. He could be driven to the point where he believes that only by taking revenge on those who wronged him and his loved ones can he set things right. This would be a very complex and angsty storyline.
If Shirou Emiya were reincarnated as a girl in fanfiction, the story could take an interesting turn in terms of romance. She might attract different suitors or have a different approach to love. Maybe she would be more reserved or more bold in expressing her feelings, depending on how the author writes her personality. And in combat, she could bring a unique feminine touch, like using grace and agility in a different way compared to her male self.
One plot idea could be Dark Shirou in a post - apocalyptic world where he uses his skills to survive and rule a small territory. Another could be his journey to find a way to reverse his dark transformation. Or a plot where he has to face his darker self in a psychological battle within his own mind.
One possible plotline could be Shirou finding himself magically transported to the Harry Potter world. He might use his skills in magic and combat from his own world to help Harry and his friends in their battles against Voldemort. For example, Shirou's ability to project weapons could be a unique advantage in the wizarding world.
A fanfic could have Shirou befriending the hobbits. He could teach them some self - defense skills using his martial arts knowledge. And in return, the hobbits could introduce him to the simple joys of Shire life. Maybe he even helps them in their quest to destroy the One Ring in some way.