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.
In fanfiction, she might run away because she has a personal family issue that she needs to deal with immediately. For example, if she finds out that her parents are in some kind of danger from the wizarding world. Or she could be following a lead on something that she believes is more important than her studies at Hogwarts, like a mysterious prophecy that she thinks can only be deciphered away from the school.
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.
Well, perhaps they ran away because they were tired of all the rules and restrictions at Hogwarts. Harry had always had a bit of a rebel streak, and Hermione might have finally agreed that they could achieve more on their own. Also, it could be related to a prophecy that they thought was best dealt with away from the prying eyes of their friends and teachers.
One possible reason could be that he discovers a dark secret about his family. Maybe he finds out that his parents were involved in something he can't accept, like a deal with a dangerous enemy. So, to avoid being associated with it, he runs away.
Perhaps he is on a quest for self - discovery. Jon Snow has always had a complex identity, and in fanfiction, he may feel that he can't fully understand himself while remaining in Winterfell. He runs away to explore the world outside, meet new people, and learn more about his true nature, which he hopes will ultimately make him a better leader or person.
One possible reason could be that Naruto feels like an outcast. Despite being part of Team 7, he might think that Sasuke and Sakura are closer to each other. Naruto has always been alone before joining the team, and if he feels excluded again, it could lead to him running away. Also, he might be afraid of endangering his teammates. Naruto often attracts trouble because of the Nine - Tails inside him. He may think that by leaving, he can keep his friends safe from the enemies who are after him for the power of the Nine - Tails.
Perhaps he runs away because he feels misunderstood. In the fanfiction, the other students or even some of the teachers might wrongly accuse him of something. He could be tired of constantly having to defend himself. Like if he was wrongly blamed for a serious incident at Hogwarts, and no one seemed to believe his innocence, he might just leave in frustration.
Perhaps he was influenced by some new friends he met who had a different lifestyle or view of the world. They might have convinced him that running away from home was an exciting adventure and a way to break free from the restrictions at home.
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.