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.
Perhaps it's an enemy character who she had an unexpected encounter with, and this led to the pregnancy. It would add a lot of drama to the fanfiction as she then has to deal with not only the pregnancy but also the implications of the father being an enemy.
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 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 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.
One possible theme could be self - discovery. Ginny running away pregnant might force her to figure out who she is on her own, away from the expectations of others.
It could be her best friend. In many stories, best friends have a special bond and can sense when something is wrong. So, her best friend might start looking for her and be the first to find her.