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'.
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.
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 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.
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'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 betrayed by the village. Maybe he discovers some dark secrets about Konoha that make him lose faith in it. For example, if he finds out that the village leaders have been using him all along without truly caring for his well - being.
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.
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.
Maybe Naruto runs away from the Sharrigan because he is framed for a crime he didn't commit. The Sharrigan - wielding enemies believe he has done something wrong and he has no choice but to flee. As he runs, he meets new allies who help him clear his name and also understand the true nature of the Sharrigan better.