One possible scenario is that Snape has created a powerful and dangerous spell or potion that threatens the safety of the wizarding world. Harry, with his sense of responsibility, takes it upon himself to stop Snape. He may engage in a fierce magical battle with Snape and, in the end, manage to destroy Snape to prevent the disaster that his actions could cause.
In such a fanfiction, perhaps Harry discovers some dark secret of Snape's that makes him decide to take action against him. Maybe Snape has been plotting something truly evil all along, and Harry finally uncovers it and has to destroy Snape to protect Hogwarts and his friends.
Perhaps in the fanfiction, there is a prophecy that Snape will cause great harm to Hogwarts. Harry, being the hero, feels it's his duty to stop Snape. He starts to gather evidence of Snape's wrongdoings, which are not obvious at first. As he digs deeper, he uncovers a web of lies and deceit that Snape has spun. This leads to a confrontation where Harry uses his magic skills and the loyalty of his friends to destroy Snape's influence over the school and the other wizards. Snape might have been planning to use dark magic to take over Hogwarts, and Harry is the only one who can prevent it.
Perhaps in this fanfiction, Harry submits to Snape in order to gain access to some important information. Snape might be in possession of secrets about Harry's family or his own powers that he refuses to share unless Harry shows complete obedience. So, Harry decides to submit to Snape's demands in order to uncover these mysteries that are crucial for his journey as a wizard.
In a more dramatic scenario, during a battle at Hogwarts. Snape might find Harry injured and touch him gently to assess his condition. This could be a very poignant moment as Snape, who has always had a difficult relationship with Harry, is now showing a side of concern. It could also lead to a new level of respect between them.
In some fanfictions, there could be a situation where Snape's true motives are being misinterpreted by the wizarding community. Harry, who has a deeper understanding of Snape's character, defends him. He could talk about Snape's unrequited love for his mother and how that love led Snape to make difficult choices. Harry may also point out that Snape was a key figure in the downfall of Voldemort, and without him, the outcome of the war would have been very different.
One possible scenario could be in a potions class. Snape might be unfairly criticizing Harry's work as usual, but this time Harry decides he's had enough. He stands up, looks Snape in the eye, and calmly but firmly defends his potion - making process, explaining how he followed the instructions correctly. This could shock Snape into silence for a moment.
Perhaps in the fanfiction, there's a curse that was meant for Snape but Harry jumps in to take it. As Harry is dying in Snape's arms, Snape has a moment of deep reflection. He might think about all the times he could have been kinder to Harry, and how Harry has now become a symbol of the good that Snape had long forgotten in his own life. And this moment of Harry's death could be a turning point for Snape's character development in the fanfiction.
Ron and Hermione would most likely be his allies. They've always been by Harry's side through thick and thin. In this situation, they would use their respective skills, Ron's loyalty and Hermione's vast knowledge of magic, to support Harry in his mission to destroy Snape.
One possible reason could be remorse. Harry might realize that he misjudged Snape all along. Snape had a complex role, and if Harry discovers the truth about Snape's true loyalties and sacrifices, it could lead to him crying out of guilt for how he treated Snape in the past.
Often, Snape will single out Harry in front of the whole class. He might publicly criticize Harry's work or attitude. For example, when Harry is assigned a group project in Potions, Snape might give Harry extra tasks or set higher standards just for him. And during exams, Snape could be extra strict when grading Harry's papers.
One interesting scenario could be that during detention, Snape makes Harry clean all the potion bottles in the dungeon while lecturing him about the importance of precision in potions. Harry, in turn, discovers an old, forgotten potion recipe among the bottles and Snape is grudgingly impressed.