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.
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.
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.
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.
It's appealing because it shows a different side of the characters. We usually see Hermione as strong and in control, so seeing her vulnerable is interesting. And Fred, who is often portrayed as the fun - loving prankster, gets to show his caring side. It also allows for new interactions between two characters who don't have a lot of one - on - one time in the original series.
One possible reason could be a misunderstanding in the fanfiction. Maybe Ron said something stupid or insensitive, like in the original series where he sometimes had a hard time expressing his feelings properly. This could have deeply hurt Hermione, leading to her crying.
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.
Often, Harry will offer her a handkerchief or a tissue if there is one available. He might also put his arm around her in a comforting gesture. In 'The Common Room Crisis' fanfic, he does just that and then stays with her, listening intently as she pours out her feelings. He is patient and understanding, which is in line with his character in the original books. He tries to make her laugh or at least smile by sharing a joke or a funny memory. This shows his deep friendship and care for Hermione.
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.
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.
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.