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.
In some fanfics, the author might want to explore a darker side of Harry. So, they create a scenario where Harry is corrupted by power or a dark object. Snape, being as prickly as he is, gets in Harry's way, and Harry, in his new, darker state, kills Snape. Or perhaps there's a prophecy that Harry misinterprets, thinking Snape is a threat to the safety of the wizarding world and thus takes his life.
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.
Perhaps in fanfic Harry complains about Snape due to Snape's relationship with his father, James. Snape clearly had a lot of animosity towards James, and sometimes that spilled over onto Harry. Harry might feel that Snape is holding a grudge against him for something his father did, which is unfair, and thus complain.
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.
Well, one possible reason could be a very extreme misinterpretation of Snape's hatred for Harry's father. If the fanfiction writer took Snape's grudge to an unrealistic level, they might write a scenario where Snape wants to destroy Harry as a form of revenge. But this is far from the nuanced relationship shown in the original books.
One possible reason could be Snape's long - standing grudge against James Potter, Harry's father. Since Snape had a difficult past with James, he might project that onto Harry. Another reason could be that Snape is trying to protect Harry in a very strange way. He may think that by rejecting Harry, he is keeping him at a distance from the dangerous wizarding world politics and plots that Snape is often involved in.
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.
One possible reason could be if Harry were to break a major school rule in the fanfic, like using dark magic without proper authorization. Dumbledore is a strict adherent to the rules of Hogwarts and would likely punish such behavior.
One possible reason could be Snape's unfair treatment of Harry and his friends. Snape often showed blatant favoritism towards Slytherin students and was overly harsh on Gryffindors, especially Harry. This constant bias could lead Harry to want him fired. Another reason might be Snape's connection to the Dark Arts. Harry, having faced Voldemort, might be worried about Snape's knowledge and use of dark magic within Hogwarts. Also, Snape's generally unpleasant demeanor towards students could be a factor. His sarcastic remarks and cold attitude might make Harry think that he is not a suitable teacher for Hogwarts students.
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.