In some fanfictions, a great plot twist is that Snape is not really who he seems in terms of his magical abilities. He might be hiding a much greater power, and Hermione discovers this during a crucial moment. This discovery makes her trust in him even stronger as she realizes he has been hiding his true self not to intimidate others but to protect the wizarding world in his own way. Also, there could be a twist where Snape and Hermione are the only ones who can access a powerful, ancient magic, and this shared ability and the secrets it holds lead to a deeper level of trust between them.
One idea could be that Snape discovers Hermione has a rare magical ability that he's secretly been researching. He takes her on as an apprentice of sorts, much to the surprise of everyone. This could lead to a series of adventures where they explore the depths of this magic together and Snape slowly starts to see Hermione in a new light.
Well, in some fanfictions, it might start with Hermione noticing Snape's hidden acts of kindness. For example, she could observe him secretly helping students in ways that others don't see. This makes her question the common perception of him as a cold and mean teacher. As she delves deeper, perhaps she discovers his more complex past and motives, gradually building trust.
One example could be 'The Unlikely Bond'. In this fanfiction, Hermione discovers Snape's hidden motives during the war and gradually comes to trust him. It shows how Hermione, with her inquisitive nature, digs deeper into Snape's actions and realizes he was not as bad as she initially thought. Another good one is 'Hermione's New Perspective'. Here, after a series of magical mishaps, Hermione and Snape are forced to work together. Through their interactions, Hermione begins to see Snape in a new light and trust is slowly built between them.
Another theme is the redemption of Snape through his interactions with Hermione. Since Snape has a rather dark past in the original series, in fanfictions, Hermione can be the catalyst for his positive change. She might see the good in him that others don't and help him come to terms with his own demons.
One plot twist could be that Snape is actually under a spell that makes him fall in love with Hermione. This could lead to a whole mystery about who cast the spell and why. Hermione would then have to figure out whether the love is real or not, while still dealing with the feelings she has developed for Snape. Another could be that they get married in secret, and when it's revealed, it causes an uproar in the wizarding community, with people taking sides either for or against their union.
One plot idea could be that Hermione gets angry at Snape for unfairly deducting points from Gryffindor. She confronts him in his office and they end up having a heated debate about fairness in the Hogwarts system. Another could be that Snape discovers Hermione is working on a dangerous magic experiment without proper authorization and she gets angry when he tries to stop her. A third idea is that Hermione overhears Snape making some snide remarks about her Muggle - born status and she angrily challenges his old - fashioned views.
A possible plot twist could be that Hermione is a half - veela. This is not related to being a Muggleborn at all. The fanfiction could show how her veela heritage affects her magic and her relationships at Hogwarts. For example, it might make her more alluring and powerful in certain types of magic, like charms. This would completely change the way her character is typically portrayed in the original stories where she was thought to be a Muggleborn.
One interesting plot twist could be that Hermione, as a Gryffindor in the original series, starts to question the values of her own house because of her newfound admiration for Slytherin. Maybe she discovers a long - lost family connection to a Slytherin family, which makes her more empathetic towards their ways. Another could be that she uses Slytherin - like cunning to solve a problem that Gryffindor bravado couldn't handle, causing a rift between her and some of her Gryffindor friends.
One interesting plot twist could be that Hermione's real family is a powerful wizarding dynasty in hiding. For example, they might have been in hiding from a dark wizard who was after their unique magical abilities. Another could be that she was adopted to protect her from a prophecy related to her future powers. Maybe she discovers that she has a connection to an ancient magical artifact that only her real family knew about, and this discovery changes her whole perspective on her identity and place in the wizarding world.
A really interesting plot twist could be that Snape was under a spell all along that made him seem so cold and distant, and Hermione discovers it. This changes the whole dynamic between them. Another twist could be that Hermione is actually related to someone from Snape's past in a way that they never expected, which brings them closer.