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 popular one might be 'A New Beginning' where the story delves into how fem Harry copes with being pregnant and on the run. It focuses a lot on her internal struggles and the challenges of finding a safe place.
I'm not sure of specific 'harry runs away pregnant fanfiction' stories off the top of my head. You could try searching on popular fanfiction websites like Archive of Our Own. They have a vast collection of fanfics, and you can use those keywords in the search bar to find relevant stories.
The Weasley family could also be of great help. Molly Weasley, in particular, has a motherly instinct. She could take Harry in and help him with the pregnancy as if he were one of her own children. The Weasley twins might also be able to create some useful magical items for Harry to use during his time away, like special potions for a healthy pregnancy or charms to keep him hidden. And Ron, as Harry's best friend, would be there to support him emotionally and physically, even if he was initially shocked by the situation.
One possible scenario in this kind of fanfiction could be that Ginny discovers she's pregnant at a very inconvenient time. For example, there might be some dark forces rising again in the wizarding world, and she fears for the safety of her child. So she decides to run away to a secluded place, perhaps a small cottage in the countryside that she discovers through some old family connections. This would also give the author a chance to explore Ginny's maternal instincts and her ability to fend for herself.
It could be that Naruto discovers something about the nature of his pregnancy that scares him. For example, he might find out that the child has some sort of special power that could put it in danger. So he runs away to figure out how to handle the situation without endangering the village or the child. He might seek out a hermit or an old sage to get advice on what to do.
One possibility could be that Stiles runs away because he's afraid of the reactions from his friends and family. Maybe he thinks they'll be disappointed or angry. He might go to a place where no one knows him to start a new life for himself and his unborn child.
In this fanfiction, it could be that Lucy is part of a society with strict rules about pregnancy out of wedlock. She runs away pregnant to avoid the shame and punishment that would come her way. As she runs, she might meet other outcasts who support her. She then has to figure out how to survive, find medical care for her pregnancy, and create a future for herself and her baby.
It could be Ron. Maybe they had a falling out or some sort of misunderstanding during their relationship, and Hermione runs away when she discovers she's pregnant. Another possibility is that it's a new character, someone she met during one of her adventures or studies. This new character could be from a different magical culture, and their relationship was a secret.
Well, perhaps Kagome runs away because she's pregnant and fears the reaction of her family or friends. Maybe she wants to protect the unborn child from some sort of danger or judgment in her original community.