One possible reason could be the stress from her studies. Hermione is always under a great deal of pressure to excel academically. Maybe she reached a breaking point due to the overwhelming workload. Another reason might be some kind of conflict with her friends. For example, if she had a big fight with Harry or Ron over something serious, it could leave her feeling broken.
Perhaps she was the target of some dark magic that affected her mentally. In the wizarding world, there are many dark spells and curses. If she was exposed to one, it could have a negative impact on her mental state, making her seem 'broken'. It could also be related to her family. If something bad happened to her Muggle parents, like they were threatened by Death Eaters, it would be very distressing for Hermione.
One possible reason could be that she was attacked by some dark creatures while on a solo adventure in the Forbidden Forest. The forest is full of dangers, and Hermione, being brave and curious, might have ventured too deep and got injured by a creature like a werewolf or a giant spider.
Snape might be suspicious at first. He might think it's some sort of trick or part of a bigger plot. However, as he observes Hermione more closely and realizes the genuineness of her situation, his attitude could gradually change to one of reluctant assistance. He might even offer some words of wisdom, albeit in his typical sarcastic way, to help Hermione regain her strength.
One possible reason could be a misunderstanding. Maybe Hermione thought Snape was involved in some dark plot against her friends. In the wizarding world, there are often secrets and deceptions, and if she got some false information, it could lead her to take such drastic action.
Snape could offer Hermione a book to distract her. Knowing her love for knowledge, a rare and ancient book about magic could draw her attention away from whatever is breaking her. It would be his way of saying that there are other things to focus on and that she can find solace in learning.
One reason could be the loss of a loved one. Maybe Harry has lost Ron or Hermione in a battle, and this has left him in a state of despair.
It could be a failed experiment in potions class. Hermione is always eager to try new things in potions, and perhaps this time it backfired, causing her some harm. And Snape would be the one to find her because it's his class.
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.
Maybe Hermione has a morning encounter with an unexpected character, like a centaur who comes to her with a warning about something that will happen during the day. This sets off a chain of events where she has to use her wits and knowledge to prepare for it while the morning unfolds around her. It could involve her running around the castle, gathering resources and allies all before breakfast.
One possible reason could be a powerful spell gone wrong. Maybe she was caught in the crossfire of a dark magic spell that Snape was either trying to counter or was involved in accidentally. Another reason might be extreme emotional shock. For instance, if she discovered some dark secret about Snape that was so overwhelming it sent her into a catatonic state.
Snape could also share some of his own experiences of being an outcast and misunderstood. He might tell Hermione that he too has faced hardships and that it is possible to rise above them. For example, 'I have been judged wrongly all my life, Miss Granger. Yet here I am, still standing. You are far stronger than you think.' This would give Hermione a new perspective and comfort her.