One popular fanfiction could be 'The Unseen Bond' where Snape stumbles upon fem Harry crying in the Forbidden Forest. In this story, it delves into the complex relationship between them as Snape is initially shocked but then shows a side of unexpected kindness.
Another great one is 'When Draco Saw Harry Cry'. This fanfiction focuses on the moment of discovery and how it changes the dynamic between them. It has some really heart - wrenching moments as Harry is dealing with his own issues and Draco has to decide how to respond.
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.
Perhaps he's feeling isolated. Even though he has friends, he often has to face his battles alone in some ways. Ginny finding him crying could be a moment of vulnerability that she witnesses, and it might be related to his feeling of being alone in the fight against the dark forces.
There's this fanfiction called 'Lily's Discovery'. It's quite interesting as it not only focuses on the moment Lily finds Snape crying but also on what led up to that moment. It gives a backstory about Snape's recent struggles in the Slytherin house and how Lily's discovery might be a turning point in their friendship. It's a must - read for fans of their relationship.
Snape's initial reaction would be one of disbelief. He has his own set of prejudices and ideas, and gay romance fanfiction is far from his realm of understanding. He might snatch the fanfiction away from Harry in a fit of annoyance. But as he sees Harry crying, he might start to wonder what in this strange piece of writing has such an emotional impact on Harry. This could lead to a very awkward and tense moment between them, with Snape not knowing how to handle the situation properly.
I would recommend 'The Cry in the Corridor'. In this fanfiction, fem Harry is crying in a corridor after a particularly difficult encounter with some bullies. Snape finds her and his first reaction is one of annoyance but as he sees her distress, he starts to feel a strange sense of protectiveness. The plot then thickens as it explores how this encounter changes their dynamic in the Hogwarts environment.
In this kind of fanfiction scenario, Snape might initially be conflicted. On one hand, he has his long - standing dislike for James Potter, Harry's father. But on the other, his sense of duty as a Hogwarts professor could kick in. He might reluctantly start to heal Harry, all the while muttering under his breath about how much trouble Harry always seems to get into, just like his father. Then, as he heals Harry, he might start to see some of Lily, Harry's mother, in him and soften a bit.
There could be a fanfiction named 'A Moment of Vulnerability'. In this, Lily finds Snape crying in the Potions classroom after a particularly harsh encounter with James Potter. It shows how Snape's pride is broken and Lily's reaction to seeing his vulnerability.