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.
It could be that Sasuke has some personal vendetta or a lead on something related to his family's past that he wants to pursue, and Naruto, being his friend, decides to go with him. Naruto doesn't want Sasuke to face it alone, and they both know that their villages won't approve of this pursuit, so they run away.
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.
One possible plot could be that Naruto and Sasuke run away to find a place where they can train without the interference of the Hidden Villages. They might be on a quest to become stronger together, away from the prying eyes of their respective villages which have different expectations of them.
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.
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.
One possible reason could be that Naruto might be afraid of the intense training Jiraiya has in store for him. Jiraiya is known for his strict and grueling training methods, and Naruto, being young and sometimes impatient, might just want to escape that for a while.
For Naruto, running away might make him more determined to prove his worth and protect his friends. He could learn to control his Nine - Tails chakra better in the face of danger outside the village. Sasuke may start to trust Naruto and Sakura more, realizing that they are his true comrades. Sakura, on the other hand, could become more independent and confident in her abilities, not just relying on Sasuke and Naruto but also being able to take charge when needed.
One possible plot could be that they run away from the Hidden Leaf Village to avoid a powerful enemy that is targeting them specifically. Maybe this enemy has some vendetta against them because of their unique abilities or past actions. They might have to rely on each other's skills and their friendship to survive in the wild and find a new place to call home.
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.
Love. Naruto may finally realize his true feelings for Hinata and want to be away from the chaos of the village to be with her in peace.