Maybe he feels misunderstood by his family. In many Naruto stories, his family situation can be complex. If he's 'godlike', he might have powers that his family doesn't understand or fears, leading him to run away to avoid conflict or being treated differently.
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.
One possible reason could be that he feels misunderstood. In the Naruto series, Naruto often faced isolation and judgment from the villagers. If this extended to his family in the fanfiction, he might run away to find a place where he is accepted. Maybe he discovers some dark secrets about his family that make him feel unsafe or betrayed.
He could become stronger on his own. Away from his family, he'll have to rely solely on himself. This self - reliance might push him to train harder and unlock even more of his 'godlike' powers. For instance, he might find new mentors or training methods that his family would not have allowed.
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 might meet an old hermit who teaches him a unique and powerful jutsu that his family never knew. This new jutsu gives him an edge and also makes him more confident in his abilities. He could then use this newfound power to help those in need, all while staying away from his family.
The family would be shocked at first. They might start to question their actions towards Naruto. If they were too strict or didn't give him enough love, they would feel guilty. For example, his father may realize that he pushed Naruto too hard to follow a certain path and now regrets it.
Adapting to a new ninja system could be a big challenge. Kumo may have different training methods, rules, and traditions compared to his home village. Naruto would need to learn and adjust quickly if he wants to survive there.
One possible reason could be that he feels misunderstood by his family. Maybe they have different expectations of him and he can't bear the pressure, so he decides to run away to Kumo to start a new life.
Perhaps Naruto feels that Kushina is being overprotective. He wants to prove his independence and go on his own adventures without her constant supervision, so he decides to run away.