There are many ways this could happen in fanfic. One way is that Harry uses his connection with Voldemort's mind. Since Harry has a link to Voldemort's thoughts, he might be able to pick up on Voldemort's doubts about Snape. And then Harry starts to investigate Snape further. He might recall some strange actions of Snape in the past, like his ambiguous loyalty during certain battles or his secret meetings with some unknown figures. Combining all these, Harry eventually realizes that Snape is a spy.
Snape could be in great danger. Voldemort might immediately try to kill him. Snape would have to fight for his life or try to escape. His status among the Death Eaters would be completely ruined, and he'd become a hunted man.
In a fanfiction scenario, Harry's actions could cause a complete breakdown in any potential for a positive relationship between them. Snape's loyalty to Dumbledore and his role in protecting Harry from the shadows would be put at risk. Harry would have to face the fact that he may have made a huge mistake. And Snape, who has sacrificed so much already, would be in an even more precarious position, both with Voldemort and in the wizarding world in general. This could lead to a chain of events that completely alters the course of the wizarding war, with far - reaching consequences for both Harry and Snape.
In the fanfic, Snape's reaction could be multi - faceted. He might start by investigating the abuse more deeply. He could use his skills as a Potions master and a former Death Eater to find out who is behind the abuse. And then, he might take steps to ensure Harry's safety. This could involve enlisting the help of other teachers or even trying to get Dumbledore more involved. He may also start to teach Harry some extra skills or give him potions to help him deal with the emotional and physical trauma of the abuse.
Snape might be secretly pleased at first, seeing as he has no love for Sirius. But then, being a teacher, he'd probably feel obliged to report it. He also might use this situation to his advantage against Sirius in the wizarding politics within Hogwarts.
At first, Harry is likely to be angry. He might feel that Snape is being unfair and targeting him. Harry has a strong sense of justice, and when he believes he's being wrongly punished, he'll be resentful.
In some fanfics, at first it gets worse. Harry might start to fear or hate Snape even more after being hurt. But as the story progresses, there could be a turning point. Maybe Harry discovers Snape's real motives behind the hurt, like if Snape was trying to protect him from a greater danger in a very roundabout way. This could lead to a begrudging respect or even an odd sort of friendship in the end.
At first, Harry might be very suspicious of Snape's kindness. After all, in the original story, they had a rather tense relationship. But as Snape continues to be kind, Harry starts to see him in a new light. He begins to trust Snape more and more.
Perhaps it's related to Harry's association with his father, James Potter. Snape had a long - standing grudge against James, and seeing Harry might bring back those bitter memories. So, whenever Harry does something that reminds Snape of James, like being overly confident or a bit of a troublemaker, he yells at him.
In some fanfics, Snape might hurt Harry out of his long - held grudges. Snape was in love with Harry's mother, Lily, and Harry being a reminder of James, who bullied Snape in school, could trigger his negative emotions. Also, Snape's loyalty to Voldemort in the earlier days in some fan - created scenarios might lead him to target Harry, who was seen as a threat to Voldemort's plans.
Snape might initially be shocked. He has always had a complex relationship with Harry. He could be hesitant at first, not fully believing Harry, but then as the story progresses, his protective instincts might kick in and he could start to investigate the abuse further.