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.
One possible reason could be the pressure he feels in Konoha. Naruto has always been an outcast in the village to some extent. People used to fear and shun him because of the Nine - Tails inside him. He might feel that running away would be a way to escape all that negative attention and find a place where he could be himself without the constant reminder of his 'otherness'.
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.
One reason could be a misunderstanding within the family. Maybe Naruto feels that his family doesn't understand his dreams or his ninja way. For example, if his family has different expectations for him, like wanting him to focus on clan duties instead of his own adventures and growth as a ninja. Another reason might be that he discovers a dark secret about his family and can't bear to be associated with it, so he runs away to find his own truth.
One possible reason could be Naruto's internal conflict. In yaoi fanfiction, the relationship is often complex. Naruto might be running away because he's confused about his feelings for Sasuke. He may not be ready to face the intensity of the relationship that the yaoi concept implies.
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 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.
Maybe he discovers some dark secrets about his family. For example, if his parents were involved in something he considered unethical in the fanfic's plot. It could be that they were part of a group with a hidden and evil agenda.
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.
Another reason could be that Naruto is being targeted by a powerful enemy within Konoha. He doesn't want to put his friends and the village at risk, so he runs away to draw the enemy away from Konoha. This would show his selfless side, sacrificing his own safety for the greater good of the village.