She could also be running away to protect the baby. There might be some sort of danger or negative influence in her current place. For example, if there are people who would harm the baby or if the society she lives in is very judgmental towards unwed mothers.
Perhaps she feels alone. If the father of the baby is not around or is not supportive, she might feel like she has no one to turn to in the village. So, she decides to run away to start anew somewhere else where she can raise the baby on her own terms. Also, she could be running away from her own responsibilities as a ninja. The pregnancy might make her question her role and future in the ninja world, and she chooses to escape from it all.
She may be running away to protect the baby. Maybe she fears that someone or something in her current environment poses a threat to the unborn child. It could also be that she wants to start anew, away from all the complications and expectations in her present life, so she decides to run away with the hope of building a better future for herself and her baby.
One possible reason could be that she feels overwhelmed by her responsibilities. In the world of Equestria, Twilight has a lot on her plate, like studying magic, taking care of Spike, and helping her friends. In fanfiction, the writer might explore the idea that she just needs a break from it all and runs away to find some peace.
Maybe she feels left out in the family. In the Encanto story, Mirabel is the odd one out not having a special gift. This could make her feel so alone and unwanted that she decides to run away.
Well, perhaps they run away because they discover some dark secrets about the wizarding world that others don't want them to know. They might fear for their lives if they stay, so they choose to flee. It could also be that they are simply seeking adventure. The daughter of Harry and Sirius might inherit their adventurous spirits, and they both decide to run away to explore the unknown parts of the wizarding world and beyond.
She might run away because of a conflict with her friends or team members. Maybe there was a misunderstanding or a disagreement that she couldn't resolve at that moment, and running away seemed like the best way to avoid further confrontation.
Perhaps in fanfiction, Harry runs away from the Dursleys because he discovers a new threat that the Dursleys won't protect him from. He realizes that he has to take matters into his own hands and leaving is the only option. Also, he could be running away because he has made some new friends in the wizarding world who offer him a better alternative to living with the Dursleys.
One reason could be that Loki feels constantly overshadowed by Thor. In the Asgardian hierarchy, Thor is often seen as the golden child. Loki, being the more complex and misunderstood one, might run away to find a place where he can be his own person without living in Thor's shadow.
One reason could be the trauma he endured during the war. He witnessed so much death and destruction that he might feel the need to escape it all. Maybe he wants to get away from the constant reminders of his friends who didn't make it.
One reason could be she feels extremely pressured by the high expectations at Hogwarts. Everyone expects her to be perfect in academics and problem - solving. Another might be that she discovers some dark secret within the school that she's afraid of, like a hidden plot by a group of dark wizards among the staff or students. Or she could be running away to protect her friends. If she believes that her presence at Hogwarts endangers Harry and Ron, she might choose to leave to keep them safe.