One possible plotline could be that Ed has been hiding her true gender to fit into a male - dominated society or group. Maybe she's afraid of being discriminated against. Another could be that she falls in love with someone who initially only sees her as a male friend, and then there's the big reveal.
In 'ed is secretly a girl fanfiction', a likely plotline is that Ed has a special talent or role that is typically associated with males in the story's setting. She keeps her gender a secret to hold on to this position. As the story progresses, her female identity might start to surface when she faces challenges that require her to be true to herself, like when she has to make a moral decision that goes against the male - only rules she's been abiding by.
Perhaps a plotline where Naruto, as a girl, has to face different challenges in the ninja world. Like, some male characters might treat her differently, either underestimating her or having romantic interests in her that she has to navigate while still trying to prove herself as a strong ninja. In this fanfiction, she could also form unique friendships with female characters that she didn't have as a boy.
One idea could be that Ed has to keep her true gender a secret while on her alchemic adventures to avoid discrimination in a male - dominated alchemic world. Another could be that she forms unique relationships with other characters who might suspect or eventually discover her secret.
One possible plotline could be Neville struggling to hide her true gender identity while dealing with the challenges at Hogwarts. Maybe she has to constantly come up with excuses for not participating in certain all - boy activities.
Perhaps a jealous rival. This person might be a male who is threatened by Ed's success or popularity. When they discover Ed is a girl, they could use this secret to try and drive her out of the group or community she's in. They might spread rumors or create problems for her.
One idea could be that as a girl secretly, Ed Elric might face different challenges in the male - dominated alchemist world. Maybe she has to hide her true identity while trying to achieve her alchemical goals.
A plotline could be that Keith is an undercover agent or spy, and being a girl would put her at risk in her mission. So she pretends to be a boy. As the fanfiction unfolds, she has to balance her real self and her false identity while also dealing with the challenges of her mission and the people she meets during it.
Alphonse could be a major supporting character. Since he is Ed's brother, he would be in a unique position to either help her keep the secret or accidentally almost expose it. Winry could also be important. She might be someone Ed could confide in or struggle to keep the secret from, especially if their relationship takes on new dimensions due to Ed's secret gender.
One possible plotline could be Timmy struggling to keep her secret while dealing with her Fairy Godparents. Maybe she's afraid they'll react differently if they find out she's a girl. For example, she might worry that they'll start treating her like a princess instead of a regular kid with wishes.
A plotline might be that Stiles got secretly married while on a trip away from his friends. When he returns, he has to figure out how to integrate his new married life into his old friendships. There could be comical moments like trying to hide his wedding ring or coming up with excuses for why he can't hang out at certain times. Also, the relationship within the marriage could be explored. Is it a marriage of convenience that slowly turns into love? Or was it a passionate love - at - first - sight kind of marriage that they now have to deal with in secret.
One possible plotline could be the two of them trying to keep their relationship hidden from Ron, Ginny's brother. Since Ron is Harry's best friend, they might be worried about how he'd react. Another could be them sneaking around Hogwarts to have private moments together, like meeting in the Room of Requirement.