She might be crying because she feels overwhelmed. Hermione often takes on a lot of responsibilities, like leading study groups or helping with Hogwarts' defense against the dark arts. If something goes wrong in one of these areas, she could break down. McGonagall might comfort her by saying that it's okay to ask for help and that she doesn't have to carry all the burdens alone.
Maybe she's homesick. Even though she loves Hogwarts, there could be times when she misses her Muggle family. In fanfiction, this can be a very emotional aspect. When McGonagall sees her crying, she could share some of her own experiences of missing home when she was a student, making Hermione feel less alone.
It's possible that Hermione has discovered some disturbing truth about the wizarding world or Hogwarts itself. This new knowledge could be too much for her to handle. McGonagall, with her years of experience, would then guide Hermione through processing this information and help her come to terms with it.
Perhaps Hermione is facing some sort of interpersonal issue. She could have had an argument with her friends, like Ron and Harry. In the wizarding world, friendships are crucial. If there's a rift in their relationship, it would deeply affect Hermione. McGonagall, being a perceptive teacher, might then try to mediate and give Hermione advice on how to handle the situation.
Perhaps he's had a falling - out with his friends. In the Slytherin house, there could be a lot of power dynamics and rivalries. If he's been betrayed by someone he thought was a friend, it would be very upsetting.
It could be that she's homesick. Even though she loves being at Hogwarts, sometimes she might miss her muggle family a great deal. Also, she might be crying because she's being bullied. There could be some students who are jealous of her intelligence and are giving her a hard time. In the fanfiction, Sirius finding her crying might lead to him becoming a sort of mentor or protector for her, helping her deal with whatever is making her sad.
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.
Another possibility is that she had an argument with a friend. It might not even be Ron. It could be with Harry or another Gryffindor. She's very sensitive about her friendships and any conflict could make her cry.
Well, it could be that he's feeling the weight of his destiny. Harry has so much on his shoulders, like fighting Voldemort. Maybe he just had a particularly tough encounter with the Dark Arts or lost someone dear in the fight against the dark side. Another reason might be his feeling of isolation. Despite having friends, there are times when he feels alone in his battle.
She might be initially shocked. After all, Draco is usually seen as this tough Slytherin. But then she could feel sympathy. For instance, she might offer him a handkerchief without saying much at first.
One great fanfiction with this scenario is 'A Chance Encounter' where Draco stumbles upon Hermione crying in the library. The story beautifully shows how his initial shock turns into concern and how they start to see each other in a new light. It's a really heart - warming read.
One great fanfiction could be 'The Unspoken Pain' where Harry stumbles upon Hermione crying in the library. It delves into the stress she's under from all the studying and the looming threats in the wizarding world. Another is 'A Moment of Weakness' which shows a more personal side of Hermione, perhaps feeling left out by her friends, and Harry is there to comfort her.
A good place to find 'Fred Finds Hermione Crying' fanfiction is on Archive of Our Own (AO3). There are many works that explore this scenario. Some fanfictions in this category might focus on the emotional side of Hermione, showing her as more than just the intelligent bookworm. Fred's reaction can vary from being shocked at first to being very empathetic, and these different portrayals make for interesting reads.