One idea could be that when Hermione turns into a boy, she has to deal with different social dynamics in Hogwarts. For example, she might be treated differently by the boys in Gryffindor. Some might be more competitive with her, while others might befriend her in a new way. In the fanfiction, it could explore how she uses her now - male identity to her advantage in magic studies, perhaps being able to participate in all - male magical dueling clubs or something similar. And she could also have an interesting time trying to hide this transformation from her professors, especially McGonagall who is very perceptive.
One idea could be that Hermione turns into a Nunbu as a result of a magical experiment gone wrong. Maybe she was trying to study a new form of transformation magic and accidentally triggers this strange transformation. Then she has to figure out how to reverse it while dealing with the unique abilities and limitations of being a Nunbu.
One idea could be that Hermione turns into a centaur as a result of a misfired spell during a Defense Against the Dark Arts class. She could then struggle to adapt to her new form, having to deal with the physical differences like running on four legs and having a horse - like body. Meanwhile, her friends Harry and Ron would be trying to find a way to reverse the spell.
Well, it's possible that her magic becomes more attuned to male - dominated magical fields. If in her normal form she was great at academic magic, as a boy she might find she has a natural affinity for combat magic. She could discover that she can learn certain spells quicker, like the more aggressive hexes and jinxes. This change in her magic could also lead to her having different magical relationships. For instance, she might attract the attention of male magical creatures that were previously indifferent to her, and they could offer her new forms of magical knowledge or assistance.
One idea could be that Hermione turns into a phoenix. She could then use her new form to fly around Hogwarts, exploring places that are usually off - limits. She might also discover she has the power to heal with her tears, like a phoenix does, and help injured students or magical creatures on the school grounds.
In a fantasy world, a boy is cursed by an evil witch to turn into a girl. To break the curse, he has to complete a series of quests. Along the way, he meets different characters who teach him about the different experiences and challenges that girls face, and he gains a new understanding and respect for the opposite gender.
A possible fanfiction plot could be that Draco, now a girl, discovers new magical abilities that were suppressed in his male form. These powers could be related to a more intuitive connection with magic, something that is often associated with femininity in the wizarding world. This newfound power could put her in a position where she has to choose between using it for the benefit of Slytherin or for the greater good of Hogwarts, creating a moral dilemma for her character.
In a Hermione turns into a Nundu fanfiction, the story could start with Hermione feeling a strange connection to the Nundu in the magical creatures' book. She becomes so intrigued that she tries to perform a spell to understand it better on a deeper level. However, the spell mutates and she transforms into a Nundu. As a Nundu, she experiences the world in a completely different way. She can't communicate with her friends as she used to. Her friends would first be shocked and then start looking for solutions in every magical book and from every magical expert they know.
Maybe in this fanfiction, Midoriya as a girl discovers new aspects of her power. Since her body has changed, the way she channels her quirk might also be different. She could then have to train all over again to master this new way of using her ability.
Another possibility is that Batman is experimenting with a new technology to enhance his abilities. He creates a device that is supposed to give him the ability to fly like a bat. However, something goes wrong during the testing phase. The device fuses with his DNA, and he starts to turn into a bat. He has to deal with the physical and mental changes, all while trying to keep it a secret from his allies like Alfred and Commissioner Gordon.
Perhaps in a parallel universe, Superman is born as a girl. This version of her grows up with different experiences and challenges. She could be more in tune with female issues in society and use her powers to fight for gender equality as well as the usual superhero stuff like saving the world from villains and disasters.