Harry could initially be in shock. He's always counted on Hermione, so her abandonment would be a huge blow. He might feel a sense of betrayal and confusion.
She could get angry. Hermione, being the strong - willed character she is, might feel betrayed that Harry is leaving. She might yell at him, asking him why he's doing this and how he could leave her after all they've been through together. Her anger is really a mask for her deep sadness and fear of losing him.
She might be initially confused. Hermione is a logical person, and without an obvious reason for Harry's silence, she would be at a loss. She would probably try to think back on their recent interactions to figure out what went wrong.
Hermione would probably be deeply hurt at first. She trusts Harry and Ron so much, and being abandoned by them would be a huge blow. But she's also very determined. So, she might throw herself into her studies even more, using her knowledge as a way to cope and also to find a solution to the situation.
Perhaps she tries to find them right away. Using her intelligence and resourcefulness, she starts to search for any clues as to where they might have gone. She could ask other friends, like Neville or Luna, if they have seen Harry and Ron. And she might be determined to bring them back, not willing to give up on their friendship easily.
In the fanfic, Harry could have a range of reactions. At first, he might be in denial, thinking that Hermione is just joking or that she will change her mind. Then, when he realizes it's for real, he could get angry, feeling like he's been unfairly judged or rejected. However, over time, he may come to accept it and focus on other aspects of his life, like his fight against the dark forces or his relationships with other friends.
He could get angry at Hermione for not believing in him. Maybe he would storm off and then later try to prove his innocence by showing her his study methods or the source of his newfound knowledge. He might also feel betrayed since Hermione is one of his closest friends and her accusation is a serious one.
Harry is usually completely devastated. He might go into a state of shock at first, unable to believe that Hermione is gone. Then he could be filled with anger, either at himself for not being able to protect her or at the situation that led to her death.
At first, Harry might be confused. He would try to figure out what went wrong. He might search his memory for any signs that could have led to this betrayal. Then, he would likely experience a range of emotions from sadness to rage. Depending on the nature of the betrayal, he could either try to win them back by showing them the truth or decide that they are no longer worthy of his friendship and focus on his own path, maybe even leaving the wizarding world for a while to clear his head.
He could be initially confused. Harry might not understand why Hermione is suddenly pushing him away. He might try to talk to her to find out the reason, but if Hermione is determined, he could be left feeling hurt and a bit lost.