One reason could be Hermione's intelligence. Snape might recognize that she is smart enough to understand his complex situation. He could see her as someone who could offer a different perspective on his problems.
One possible reason could be a misunderstanding. Maybe Hermione thought Snape was involved in some dark plot against her friends. In the wizarding world, there are often secrets and deceptions, and if she got some false information, it could lead her to take such drastic action.
One possible reason could be Snape's unfair treatment of Gryffindor students. Hermione, being a strong advocate for justice, might not tolerate his constant jabs at her house. For example, in the original story, Snape often took points from Gryffindor without what Hermione might consider proper cause. In fanfiction, this could be exaggerated, leading to her blowing up at him.
It could completely transform their relationship. Initially, they had a rather strained relationship due to Snape's often harsh demeanor and Hermione being a Gryffindor. But once he confides in her, she may feel a sense of responsibility towards him. This could lead to her defending him in certain situations. Snape might also open up more about his past and his reasons for his actions, which would make Hermione more empathetic towards him.
One possible reason could be the stress from her studies. Hermione is always under a great deal of pressure to excel academically. Maybe she reached a breaking point due to the overwhelming workload. Another reason might be some kind of conflict with her friends. For example, if she had a big fight with Harry or Ron over something serious, it could leave her feeling broken.
One possible reason could be a powerful spell gone wrong. Maybe she was caught in the crossfire of a dark magic spell that Snape was either trying to counter or was involved in accidentally. Another reason might be extreme emotional shock. For instance, if she discovered some dark secret about Snape that was so overwhelming it sent her into a catatonic state.
One possible reason could be that Snape has shown unexpected kindness to Hermione in the fanfiction. Maybe he has protected her from some danger secretly, which makes her feel she can rely on him and thus feel safe.
Maybe Snape is involved in some sort of mystery or danger within Hogwarts that has to do with magic spells. Hermione, with her vast knowledge of spells and her in - depth study of the Hogwarts library, could be a great help to him in deciphering old spells or magical texts related to the situation.
One possible reason could be related to a difficult potion she's trying to brew. Snape is a potions master, and Hermione might be facing an ingredient or a process that she can't figure out on her own. For example, a rare potion that requires precise handling of dangerous ingredients.
It could be a failed experiment in potions class. Hermione is always eager to try new things in potions, and perhaps this time it backfired, causing her some harm. And Snape would be the one to find her because it's his class.
Maybe she's tired of the often inaccurate portrayals of the characters. Fanfiction sometimes distorts the true nature of Hermione and Snape's relationship as it was in the original books. For example, some fanfictions might make their interactions overly romantic when in fact they were more complex and often adversarial in the canon.