Maybe he's running away from the pressure in the village. There are always high expectations on him, and he might feel suffocated and need some time alone to figure things out.
In fanfictions, Naruto could run away from his family due to emotional abuse. If his family members constantly put him down, criticize his abilities, or make him feel unworthy, he'd likely want to escape. Also, if his family is involved in some political intrigue that he doesn't want to be dragged into. For instance, they might be making deals with other clans that Naruto disagrees with. Additionally, if there is a new family member introduced, like a step - sibling who is favored over him and he feels unloved, that could prompt him to run away.
They might run away to avoid a conflict that their villages are about to be dragged into. Naruto and Sasuke, being the powerful ninjas they are, don't want to be used as tools in a war, so they decide to run away.
Perhaps Naruto discovers something about Itachi that the rest of the world doesn't know and he needs to run away to protect that secret. It could be a powerful jutsu or a message that could change the balance of power in the ninja world.
Perhaps he is running away from danger in Konoha. There could be a threat that he believes he can't face directly in the village, and he thinks Whirlpool might offer some sort of sanctuary or a way to become stronger in relative safety.
Maybe he's running away from some kind of danger or threat in his home village. There could be a group or an individual after him, and he believes that Kumo would be a safer place. It could also be related to some political unrest in Konoha that makes him feel like he has to leave, and Kumo seems like a viable option.
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.
Sakura can also be a common character. She could be worried about Naruto and try to find him. Maybe she has her own reasons for wanting to bring him back, like her feelings for him or her loyalty to the village.
It could be a rogue ninja from another village who wants to capture Naruto and Ino for their own gain. Maybe he heard about Naruto's Nine - Tails power and Ino's family's special techniques and plans to sell them to the highest bidder.