She might be initially confused. Hermione is a logical person, and without an obvious reason for Harry's silence, she would be at a loss. She would probably try to think back on their recent interactions to figure out what went wrong.
One possible reason could be a misunderstanding. Maybe Harry overheard Hermione saying something that he misinterpreted, like she was criticizing his actions but in reality she was just worried. For example, if Hermione was expressing concerns about Harry's risky adventures in a way that Harry thought was her doubting his abilities.
It could also be that the plot of the fanfiction has Naruto in a situation where talking might put him or his loved ones in danger. So, for their safety and his own, he chooses not to talk.
This situation can also deepen Naruto's character. His refusal to talk can be seen as a sign of his growth, perhaps he has become more cautious or self - aware. And this new aspect of his character can influence how other characters interact with him, and ultimately shape the direction of the entire fanfiction.
She might be heartbroken. Ginny could initially be in shock and disbelief. She may retreat into herself, spending a lot of time alone in her room, crying and trying to understand why Harry would refuse.
One reason could be to explore an alternate path for Hermione's character. By having her refuse the prefect position, it shows a different side of her independence and her ability to make choices that go against the norm in the Hogwarts hierarchy.
I'm not sure specifically which 'Hermione refuses prefect' fanfictions are out there. You could try searching on fanfiction platforms like FanFiction.net or Archive of Our Own. Just type in the relevant keywords in their search bars and see what comes up.
They might be really curious about the creativity of Muggles. Hermione could say that it's interesting how Muggles can create their own stories based on different universes. Harry might add that he's amazed at the variety of ideas in Muggle fanfiction.
He could also be heartbroken. Ron might withdraw into himself, spending a lot of time alone in his room at the Burrow, not wanting to talk to anyone. He may start to doubt his self - worth, thinking that he wasn't good enough for Hermione.
One possible reason could be that in the fanfiction, Hermione has different career aspirations. She might be so focused on her magical research or her work in the Ministry that she feels marriage would hold her back. For example, she could be on the verge of a major discovery in the field of spell - modification and doesn't want any distractions.