In the fanfic, it could be that Snape has a change of heart due to seeing Harry's struggles. Harry may be facing some great challenges that make Snape empathize with him. Snape, having been through his own difficult times, might then decide to put aside his previous animosity and help Harry instead.
One possible reason could be that in the fanfic, Snape realizes Harry has more of Lily in him than he initially thought. Harry might show kindness or a particular trait that reminds Snape of Lily, softening his feelings.
Perhaps in this fanfic, Snape discovers a hidden connection between him and Harry that has nothing to do with James Potter. This newfound connection makes him see Harry in a different light, not as the son of the man he hated but as an individual with his own merits.
One possible reason could be that in the fanfiction, the author might explore Snape's complex past with Harry's mother, Lily. Snape's love for Lily could translate into a more nuanced view of Harry. He may see parts of Lily in Harry and that softens his hatred.
One possible reason could be his lingering resentment towards James Potter, Harry's father. Snape and James had a long - standing feud during their school days. Since Harry looks a lot like James, Snape might be transferring his old grudges onto Harry.
One reason could be to save him. Maybe Harry is injured during a battle or some sort of magical accident, and Snape, despite their differences, steps in to carry him to safety. For example, if Harry is hit by a dark curse and Snape, with his knowledge of dark magic, knows he needs to get Harry to the infirmary quickly.
One reason could be jealousy. If in the fanfiction Snape is getting more attention or praise from the wizarding world than Lily, she might start to dislike him. Another reason could be that Snape has a different view on blood purity, and Lily strongly disagrees with him, which leads to her hatred.
In this fanfiction scenario, Snape may become protective of Hermione because she might be involved in some important magical research or discovery. Snape, being a knowledgeable wizard, realizes the significance of her work and decides to protect her from those who might want to stop or steal her ideas. Also, Hermione could be in the middle of a conflict between different wizarding factions, and Snape, for his own reasons, decides to side with her and keep her safe.
One possible reason could be Snape's long - held grudges and resentments. He has a complex history with Harry's father, James Potter. Snape might see too much of James in Harry and be unable to separate the two, thus rejecting Harry despite any potential father - son connection. Another reason could be Snape's own self - loathing and his belief that he is not worthy or fit to be a father figure. He may think that he would only bring harm or a bad influence to Harry's life.
One possible reason could be that Snape is still holding a grudge against James Potter, Harry's father. He might take out his long - standing anger on Harry. Another reason could be that Snape is trying to discipline Harry in his own strict way, but it ends up being too harsh and making Harry cry.
In some fanfics, Snape might punish Harry because of his perceived insolence in class. Harry has a rebellious streak, and Snape, being strict, wouldn't tolerate any behavior that he deems disrespectful to his authority as a teacher.
Maybe in the fanfic, Snape is written as having some hidden, truly evil motives that Harry discovers, leading him to kill Snape. For example, if Snape was secretly working for a new dark force even worse than Voldemort.
One common reason is Snape's lingering hatred for James Potter. Since Harry looks so much like his father, Snape might take out his old grudges on Harry. He sees James in Harry and can't help but be reminded of the past bullying and his unrequited love for Lily. So, he acts hurtfully towards Harry as a way to get back at James, even if it's not really fair to Harry.