Maybe he's running away from the pressure in the village. There are always high expectations on him, and he might feel suffocated and need some time alone to figure things out.
One consequence could be that his friends worry about him a great deal. They might go on a search for him, which could put them in danger as well. After all, they care about Naruto deeply and won't just let him disappear without trying to find him.
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.
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.
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.
The story may develop with the village realizing she's missing and sending out search parties. Some characters might be sympathetic to her situation and try to help her secretly. Meanwhile, she has to deal with the physical and emotional challenges of pregnancy alone. After the baby is born, she may start training the baby in secret ninja skills while trying to keep their existence hidden from the world that might want to use or harm them.
A kind stranger could come to his aid. Maybe someone who has been through a similar situation in the past. This person could offer practical advice on how to survive while being on the run and pregnant. They might also teach Stiles some skills like cooking healthy meals for the baby's sake.