Snape might simply sit with Harry in silence for a while. Just his presence could be reassuring to Harry. After some time, Snape could start a conversation, asking Harry what is wrong in a more empathetic tone than usual. This gradual approach could help Harry calm down.
In fanfiction, Snape could also use his knowledge of the Dark Arts to protect Harry from whatever is causing him distress. If it's some sort of dark magic or a malevolent force that is making Harry cry, Snape could use his skills to counter it. By doing so, Harry would feel safe and stop crying as the threat is removed.
Perhaps Snape would share some of his own past experiences with Harry to make him feel less alone. For example, he could say something about how he overcame difficult situations when he was young, which might give Harry the strength to stop crying. He might say, 'I too faced hardships, Potter, and I did not allow myself to break down like this.'
Snape could begin by apologizing for his past behavior towards Harry. This would be a huge step in gaining Harry's trust. Then, he could start mentoring Harry in a more positive way. He could share his own experiences of dealing with dark magic and difficult situations. Snape could also introduce Harry to some of his old contacts or resources that could be useful for Harry's development. For instance, some old books or spells that are not commonly known but could help Harry become stronger both magically and emotionally.
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.
Isolation. Snape is a lonely character. He doesn't have many friends, and he is constantly in a difficult position between the Death Eaters and the Order of the Phoenix. His feeling of being alone and not being fully understood by anyone can lead to crying in fanfiction.
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.
Well, it could be due to the stress of their relationship. Harry had a lot on his plate, being the hero and all. Ginny was also a strong - willed witch with her own ideas. They might have had an argument about their future together. For example, Harry might be worried about Ginny's safety if they stayed together, given his dangerous life. Ginny, on the other hand, could be frustrated that Harry was trying to push her away for her own good. Another possibility is that they could be crying over the state of the wizarding world. After all the destruction caused by the war, seeing their beloved Hogwarts in ruins or the wizarding community divided could be heart - breaking for them.
Well, in a fanfiction scenario where Snape finds crying Harry, there are so many possibilities. Snape could be secretly pleased that Harry is showing vulnerability, as he has always seen Harry as James Potter's son. But on the other hand, he might also feel a twinge of guilt for how he's treated Harry. The encounter could spark a whole new storyline. For example, Snape could start to protect Harry more secretly, or he could use this as an opportunity to finally have an honest conversation with Harry about their complicated past and present situation.
Another plotline could be that there is a spell or a magical occurrence that forces Snape and Harry to be close to each other. Initially resistant, Snape eventually gives in and cuddles Harry. This could then be the start of a journey where they learn to trust and rely on each other more.
Well, one possible plotline could be that Snape is examining Harry for some sort of magical ability or deficiency that he suspects. Maybe he's trying to figure out why Harry has such an affinity for certain spells. Another could be that Snape is examining Harry as part of a school investigation, perhaps related to some mischief that's been going on. And it could also be that Snape is secretly examining Harry to protect him from some hidden danger in the wizarding world.
In some fanfictions, Snape might use his deep knowledge of magic to create a calming spell or potion specifically for Harry. For example, he could brew a special tea with calming herbs that he forces Harry to drink, and as the warm liquid goes down Harry's throat, he starts to feel more at ease.