He could be influenced by a powerful and mysterious force. This force might be something magical or a very strong jutsu that causes him to lose his memory and wander away from his family. In some fanfics, new and made - up powers can often play a role in such situations. Without his memory, he doesn't recognize his family and just drifts away.
Perhaps he discovers something about his past or his powers that makes him feel he has to leave Konoha to explore it further. For example, he might find out about a hidden place related to the Uzumaki clan and wants to go there alone to uncover the secrets. Or it could be that he has some kind of internal conflict within himself, like feeling unworthy of being in Konoha due to some self - perceived failure, and so he runs away.
In some fanfics, Naruto might leave his family because of a dangerous threat approaching them. He could believe that by leaving, he would draw the danger away and keep his family safe.
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.
One possible reason could be for the sake of creating a dramatic plot. The disappearance of Naruto might be used to show how the female characters respond to his absence, highlighting their growth and independence. For example, Sakura might take on more leadership roles in the village without Naruto around.
One reason could be that he wants to seek independence. Naruto has always been a bit of an outcast in his family, and he might feel that moving out is a way to prove himself and grow on his own. He could also be tired of the family drama or conflicts that might exist within the family unit in the fanfic.
It could also be due to power struggles within the family. Naruto's growing power might threaten the existing power balance in the family. Some family members, fearing a loss of their influence, decide to reject Naruto to try and keep their power. For instance, if Naruto has a unique ability that could potentially change the family's long - established ways of doing things.
Naruto could be afraid of being seen as weak. In the ninja world, weakness is often frowned upon. He has a reputation to uphold, especially in front of his family. He doesn't want them to think that he can't handle his problems, so he hides his pain. He also might be trying to be strong for his family. If they see him in pain, it could affect their morale. So, he pretends that everything is okay to keep their spirits high and to give them the impression that they can rely on him no matter what.
It could also be due to a lack of support. Naruto was constantly in trouble and trying to prove himself. If his family didn't show up in any way to support him and Konoha didn't do enough to encourage him in a positive way, but rather just punished him for his pranks, he might grow to hate them both.
One possible reason could be some kind of dark magic or jutsu that has affected his family's memories. Maybe an enemy cast a spell specifically to make his family forget about him to weaken him.
One possible reason is that she is in danger. There could be someone or something that wants to harm her or her unborn child, so she has to disappear to stay safe.