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.
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.
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.
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.
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.
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.
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.
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.
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.