He could run to the Forbidden Forest. It's a place full of mystery and danger, but also a good hiding place as it's vast and not many people would expect him to be there. He might find some solace among the magical creatures there.
One reason could be fear. Snape has always been rather intimidating to Harry. Snape's cold demeanor and his past interactions with Harry's father might make Harry feel constantly on edge around him. So, running away could be an instinctual response to this fear.
One possible reason could be that Harry is afraid of Snape's intimidating presence. Snape has always been strict and rather unfriendly towards Harry in the original series, so in the fanfiction, this fear might be amplified, causing Harry to run. Another reason could be that Harry has stumbled upon something he shouldn't have seen that involves Snape, and he's running to avoid getting caught.
There's a fanfic titled 'Escape and Rediscovery'. Female Harry Potter runs away after feeling betrayed by some of her so - called friends at Hogwarts. She travels far and wide, learning different forms of magic from various sources. It has a really unique plot and great character development.
Perhaps Snape uses magic to create a distraction at the Dursleys' place. He could make strange noises or apparitions that scare the Dursleys, and while they are in a panic, he grabs Harry and disapparates. This would be a quick and efficient way for him to rescue Harry.
He might first find a place to hide, like an abandoned building. There, he starts to realize how difficult it is to be on his own. He has to find food and water by himself.
The whole dynamic at Hogwarts would be disrupted. His friends would be worried sick. Ron and Hermione would probably set out to find him. Without Harry, Hogwarts would seem less safe to the students. They look up to him as a symbol of hope against dark forces.
One possible theme could be self - discovery. Harry, being in such a difficult situation, might go on a journey to find out more about himself and what he truly wants. Another theme could be facing consequences. Running away while pregnant has its own set of challenges and consequences that he would have to deal with.
One idea could be that Fem Harry Potter runs away because she feels suffocated by the expectations placed on her at Hogwarts. She might head to the Forbidden Forest where she discovers a hidden magical community that has been living in seclusion. This new community could teach her different forms of magic that she was never exposed to at school.
Hermione could be involved. She might be the one who tries to stop Harry from running and encourages him to face Snape. Or she could be the one who helps Harry to hide from Snape, using her intelligence and knowledge of spells. Ron is also a likely character to be involved. He might be with Harry when he starts running and together they try to figure out what to do about Snape.