Perhaps she is being chased by some unknown enemies in Konoha who are after her for some reason. She might think that running away from Konoha is the only way to protect herself and those she cares about. It could also be that she has a new mission or purpose that she believes can only be achieved outside of Konoha, and she is willing to sacrifice her life in the village for it.
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.
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'.
Maybe he's tired of his restricted life. In the story, he might be feeling suffocated by all the rules and expectations placed on him, so he decides to run away to find freedom.
One possible reason could be that Naruto feels misunderstood in Konoha. Maybe some villagers still hold grudges against him despite his efforts to protect the village. He might run out to find a place where he can truly be accepted for who he is.
Another reason could be that Harry in the fanfic has a newfound sense of self - worth. He realizes he doesn't deserve the horrible treatment from the Dursleys and decides to break free. He may have learned about his true heritage in a different way in the fanfic and decides to leave behind the Dursleys, who have always tried to suppress his wizarding identity.
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.
It could also be that they run away to pursue a personal goal. Naruto has always wanted to find a way to truly bring peace to the ninja world and Sakura believes in his vision. So they run away from the village to seek out a powerful jutsu or a long - lost artifact that could change the fate of the ninja world for the better.
To change her character dynamics. In fanfiction, if she's not from Konoha, her relationships with characters like Naruto and Sasuke will be different. Maybe she has a different loyalty or a different set of goals that are not related to Konoha's well - being.
One reason could be that he feels misunderstood by the villagers. Despite all he has done for Konoha, some still hold grudges or are afraid of his power. Another might be that he wants to explore the world on his own terms, away from the responsibilities and restrictions of Konoha. Maybe he also feels a sense of loneliness there, as he has lost many important people and the village constantly reminds him of those losses.
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.