There could be a plot where Shirou's transformation into a girl is part of a grander scheme by an enemy. The enemy thinks that by changing his gender, they can disrupt his connection with his powers or his relationships with his allies. However, Shirou discovers that being a girl actually gives him some new powers or abilities that he didn't have before. He then uses these to turn the tables on the enemy and prove that his identity and strength are not defined by his gender.
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 interesting plot could be that Shirou, as a girl, is mistaken for a long - lost princess or some other important female figure. This leads to him being dragged into political intrigues or quests that he wouldn't have been involved in as a male. He then has to use his wits and combat skills, which are still there despite the change in gender, to navigate these new situations. Also, his relationships with the other servants could be completely rewritten. Some might be more protective of him, while others might be more suspicious.
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.
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.
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.
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.
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.
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.
In such a fanfiction, Shirou - turned - Avenger could be on a path of vengeance against those he believes have wronged him or his loved ones in the past. This could lead to a series of intense battles where he uses his new - found powers in a more brutal way compared to when he was just Shirou. And his relationships with other characters would also change drastically, like with Rin or Saber, who might be initially shocked and then try to bring him back to his former self.
Cloud could develop more empathy as a girl. Since society often expects different behaviors from females, she might start to see things from a different perspective. For instance, she may become more in tune with the feelings of others and be more nurturing. This would be a big change from her perhaps more stoic male self.
One idea could be that Danny turns into a girl due to a ghostly spell gone wrong. In the fanfiction, he could struggle with the new body while still having to fight ghosts. Maybe his friends don't recognize him at first, leading to some comical and tense situations.