One possible reason could be for Naruto's safety. Maybe she has to go on a dangerous mission and believes Konoha is the safest place for him. Another reason might be that she is forced by some powerful enemies who threaten Naruto's life if she doesn't leave him in Konoha.
In a 'naruto and kushina leaves konoha fanfic', perhaps they leave due to a threat to Naruto's safety that the village can't fully protect against. Maybe some secret organization is after him and they feel they have no choice but to go into hiding outside Konoha.
The relationship between Konoha and the Uzumaki clan might be further strained. With Kushina leaving, Konoha would lose an important link to the Uzumaki. And other Uzumaki members might see this as a sign that Konoha is not a safe place for them.
He may face some difficulties in understanding his identity. Since Kushina is not there to tell him about his family background, he might have to discover it on his own, which could lead to some misunderstandings and challenges. Also, his relationships with other characters in Konoha could be different. For example, he might seek more father - like figures among the villagers, which could change the dynamics of his interactions with them.
Naruto would probably feel abandoned at first. He might become more withdrawn and have trust issues. But as time goes on, he could grow stronger out of a need to prove himself. He may also form closer bonds with his friends in Konoha, like Sasuke and Sakura, as they become his new family in a way.
One possible reason could be for his safety. Konoha is a well - protected village with many skilled ninja. She might believe that leaving him there would ensure he has the best chance at survival and growth as a ninja. Also, she may have some mission or obligation that forces her to leave him behind, perhaps something related to the greater good of the village or the ninja world in general.
One possible reason could be to protect Naruto from the hidden threats in Konoha. Maybe she discovers some dark secrets or plots within the village that she believes will endanger Naruto, so she decides to take him away.
They might leave because of a prophecy. If there was a prophecy that Naruto would bring destruction to Konoha or that Konoha would bring destruction to Naruto, Kushina might take Naruto away to prevent it.
Maybe there are some dark secrets within Konoha that he discovers in the fanfic. These secrets could be related to the treatment of certain individuals or something more sinister about the village's leadership. Discovering such things could make Naruto decide to leave in order to distance himself from the corruption or unfairness.
Sakura would probably be very worried. She has always cared about Naruto deep down, so she might be constantly trying to find a way to bring him back. Kakashi, on the other hand, would likely understand Naruto's reasons to some extent. He might be sad but also respect Naruto's decision. As for Sasuke, if he is in the village at the time, he could be conflicted. He and Naruto have a complex relationship, and Naruto's leaving might make him realize how much Naruto actually means to him.