Another possibility is that the main antagonist could be some sort of ancient evil that is awakened by the events in the fanfic. Dumbledore might have given Snape to Harry because he sensed this new threat. This ancient evil could have powers that are unknown to the modern wizarding world and it would be up to Harry and Snape to figure out how to defeat it.
One possible plot development could be that Dumbledore gives Snape to Harry as a sort of guide in the wizarding world. Snape, with all his knowledge and experience, could show Harry things that Dumbledore couldn't. This might include some dark arts knowledge that could be used against Voldemort. It could also be a test for both of them. For Snape, to see if he can truly be selfless in helping Harry, and for Harry, to learn to trust Snape despite their past differences.
One possible plot development could be that Harry initially struggles with having Snape under his 'command' in some way. Since they had a very strained relationship in the original series, Harry might be hesitant to trust Snape even if Dumbledore has given him this new role. He could start by trying to figure out Snape's true intentions.
It could be a very complex relationship. Harry has always had a deep - seated hatred for Snape due to Snape's treatment of him in the past. But with Dumbledore's action, Harry might be forced to see Snape in a new light. At first, it could be full of suspicion and wariness on Harry's part.
In the fanfiction, Snape could protect Harry from Dumbledore by using his skills in potions. For example, he might create a potion that hides Harry's magical signature from Dumbledore's detection. Or he could use his knowledge of the Dark Arts to counter any spells or charms that Dumbledore might use to keep tabs on Harry. Snape is very intelligent and resourceful, so he could find various ways to physically and magically shield Harry from Dumbledore.
Well, perhaps one of the other teachers might have noticed Snape's behavior towards Harry and reported it to Dumbledore. It could also be that Dumbledore, being as perceptive as he is, noticed Snape's extra harsh treatment of Harry during their interactions in the corridors or in class.
One reason could be that Snape has his own complex sense of loyalty. He may feel that Dumbledore's plans for Harry are too dangerous or not in Harry's best interest in some ways. He has a long - standing relationship with Harry's mother, Lily, and perhaps through that connection, he wants to safeguard Harry from any harm that might come from Dumbledore's actions or decisions.
There are indeed. Fanfiction often takes the existing characters and relationships and turns them on their heads. In this case, Snape helping Harry against Dumbledore could be a result of Snape's long - held grudges against Dumbledore's actions or decisions. It's a creative way to explore the gray areas of these beloved characters.
Snape could say it was part of a complex experiment to understand the nature of magical essence. He might believe that by turning Harry into a girl, he can study how a person's magic changes with their physical form. Or perhaps he thought Harry needed to experience life from a different perspective to grow as a wizard, so he used a spell to transform him, using some convoluted magical theory as an excuse.