Well, he could meet new friends or allies who help him grow stronger. For instance, he might encounter a group of outcasts who understand his situation and teach him new skills or ways of thinking.
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 dangerous or unethical in the wizarding world, and he can't bear to be associated with it, so he runs away.
Naruto might rely on his ninja skills that he's learned. He's a resourceful character, so he'd use his stealth and combat abilities to find food and shelter. For instance, he could hunt small animals in the forest and build a simple shelter using his knowledge of basic survival techniques.
In a Naruto fanfic where Naruto runs away from Kushina, it could be due to various reasons. Maybe he feels misunderstood. For example, Kushina might be too strict with him in the fanfic's storyline, not allowing him to pursue his own ninja way freely, so he decides to run away to find his own path and prove himself.
He could go to Hogwarts early. Since he has some connection to the school already through his parents, he might think that the school could be a safe haven. There are also his friends' families there, like the Weasleys, who might take him in.
He could be running away because of false accusations within the family. Just like how he was wrongly judged by the village in the original story, if his family wrongly blames him for something he didn't do, like stealing a family heirloom or causing harm to a family member accidentally, he might choose to run away rather than face their unjust wrath.
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 plot could be that Naruto feels constantly overshadowed by his family's expectations. Maybe his family is full of powerful shinobi and they expect him to be just as great immediately. He runs away to find his own path and prove himself on his own terms. Along the way, he meets new friends who are also outcasts and together they form a sort of 'family' that accepts him for who he is.
It might be that his family is overprotective. Naruto is a very independent character. If his family in the fanfiction is constantly trying to hold him back from taking risks or going on adventures, he may feel suffocated. Running away would be his way of breaking free and exploring the world on his own terms.
He could meet other rogue ninjas. These are ninjas who have left their villages for various reasons, and they might be on a similar journey as Naruto. They could either help him or try to take advantage of his situation.