Another reason might be that she was cursed. Curses in the Harry Potter universe can be very difficult to remove. Snape's familiarity with the Dark Arts, whether from his past associations or his research, could give him the edge in finding a way to break the curse and heal Hermione.
Perhaps she was poisoned. There are many dark potions and substances in the wizarding world. It's possible she accidentally ingested something or was targeted by an enemy. Snape, being a master of potions, would be the most likely person to figure out the antidote and heal her.
Well, one possible scenario could be that in the fanfiction world, there are dark wizards or forces targeting Hermione for her knowledge or power. Snape, with his skills and knowledge of the dark arts, could use his magic to shield her from attacks. For example, he could set up protective spells around her when she is studying in the library or traveling around Hogwarts.
Perhaps she's being bullied. In the wizarding world, there could be other students who pick on her because she's a 'Mudblood'. This could be really distressing for Hermione, and when Snape finds her crying, he might be conflicted between his general dislike for Gryffindors and his sense of justice.
One possible reason could be that Snape sees Hermione's value as a brilliant student. He might recognize her potential and not want it to be wasted just because of her dad's actions or situation. Maybe he has a sense of justice deep down, despite his often cold exterior.
Well, in some fanfictions, Snape might use his advanced potions knowledge. He could brew a special healing potion for Hermione. Maybe it's a modified version of a known potion, like the Essence of Murtlap that has strong healing properties.
Hermione could be hiding her pregnancy from Snape because she's not sure of his feelings towards her. There may be an ambiguous relationship between them. She might be in love with him, but not sure if he feels the same. And she doesn't want to burden him or make things awkward between them. Or perhaps she suspects that Snape might be involved in something dangerous, and she doesn't want her unborn child to be dragged into it.
One possible plot could be that Hermione is facing extreme pressure from her studies at Hogwarts. Snape, despite his usual gruff exterior, notices her distress. He might start by giving her some advice on potion - making, which is his area of expertise. For example, he could subtly guide her on how to improve her Felix Felicis brew. This small act of kindness could be the start of their unique bond, where Hermione gradually finds comfort in Snape's no - nonsense approach.
One reason could be Snape's sense of duty. As a teacher at Hogwarts, he has a responsibility to look after the students, even if they attack him. So, he would put aside his personal feelings and help Hermione.
Maybe Snape made a snide comment about Hermione's intelligence or her Muggle - born status. Snape has a rather acerbic tongue, and if he said something derogatory about Hermione's abilities or her heritage, she would surely be furious. After all, Hermione works extremely hard to prove herself in the wizarding world and any attack on her intelligence or background would be a big blow.
One possible reason could be that Snape has some hidden knowledge or magic that allows him to communicate in such a way. Maybe he's trying to protect Hermione secretly and this mind - talk is a discreet way to give her advice without others noticing.
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.