It could be due to a perceived betrayal. Suppose Naruto discovers some dark secrets within his family that he can't overlook. In his 'godlike' state, he might be more morally rigid and thus decides to disown them. For instance, if he finds out that his family was involved in some unethical ninja practices in the past, he would feel compelled to distance himself.
The plot could develop with Naruto creating his own new 'family' of sorts. He might gather like - minded ninjas who understand his vision. For example, he could team up with ninjas from other villages who also strive for a new kind of ninja world order.
One possible reason could be that his newfound 'godlike' powers make his family feel estranged. They might not understand his sudden transformation and the magnitude of his power, which creates a sense of fear or discomfort, leading them to ignore him.
Well, in some fanfictions, a 'godlike' Naruto might become overconfident. His newfound power could make him act without considering his family's values or traditions. For example, he might use extreme and unethical means to achieve his goals, which his family would not approve of, thus dishonoring them.
One reason could be that Naruto has been through a lot of hardships related to his family in the fanfic. Maybe they didn't support his growth to this godlike state, or they tried to use his power for their own gain. For example, if his family had always been jealous of his potential and when he finally reached this ultimate power, he realized their true nature and decided to cut ties.
It could be about Naruto achieving god - like powers and then getting involved in situations where his actions seem to go against his family values. Maybe he makes decisions that put his family at risk or goes against their wishes due to his new - found power.
His father might be extremely disappointed. As a former Hokage, he would have expected Naruto to uphold the family's honor. His mother would probably be heartbroken, having always believed in Naruto's good nature.
Naruto's reaction could be complex. He is likely to be deeply saddened by the betrayal of his family. But being Naruto, he won't let this setback keep him down for long. He will probably start to think about the bigger picture. His 'godlike' powers come with a great responsibility, and he may feel that he has a new mission now that he is banished. He could start looking for others who are in need of help, using his powers for good in the wider world. He might also start to question his family's values and beliefs, realizing that they may not be as just as he once thought, which could lead to a change in his own perspective on family and loyalty.
It could also be due to some external influence. Perhaps an enemy manipulated Naruto's mind in the fanfiction, making him see his family in a negative light. This enemy might have used some form of mind - control or false memories to turn Naruto against his family.