Perhaps Naruto's parents were cursed or had some sort of premonition about a great danger coming to Naruto if he stayed with them. They believed that by separating from him, he would have a better chance of survival. Fanfiction writers often explore these kinds of emotional and complex scenarios to give a different perspective on Naruto's origin.
One possible reason could be that Naruto was taken for his special chakra. In the Naruto universe, his chakra is unique as he is the jinchuriki of the Nine - Tails. Some evil forces might want to control or study his chakra, so they take him from his parents. Another reason could be related to a prophecy. Maybe there are those who believe Naruto will bring great change, either good or bad according to their perspective, and they take him to try and influence his future.
One possible reason could be that they are too involved in their own shinobi duties. The world of ninjas is full of dangerous missions, and they might be constantly away on important tasks, leaving Naruto feeling neglected.
It could also be due to a prophecy. Suppose there's a prophecy that Naruto will bring great disaster in the future. His parents, believing in the prophecy, might decide to disown him in an attempt to avoid that future. They might think that by cutting ties with him, they can somehow change the course of events.
Another possibility is that Naruto has his own plans and goals that he wants to achieve independently. His true power might be a key factor in these plans, and he doesn't want his parents' influence or interference. He wants to prove himself on his own terms, without relying on his family connection.
Perhaps in this fanfiction, there is a prophecy about Naruto. Some people might believe that Naruto will bring great change, either good or bad, to the ninja world. Those who want to prevent the 'bad' change or those who want to accelerate the 'good' change might kidnap him from his parents. They think they can influence Naruto's upbringing and future actions according to their own desires.
One possible reason could be a plot by an enemy to undermine Naruto's legacy. By taking the heir name, they can create confusion and disrupt the line of succession in Konoha. It might also be part of a political maneuver within the village, where some faction wants to gain control over Naruto's influence through his heir's name.
In this fanfiction, it could be that Naruto's parents were under some sort of mind - control. Some evil entity could have taken over their minds and made them feel hatred towards Naruto. Also, it might be related to a family secret or feud. There could be something in the family's past that made them believe Naruto was a stain on their family name, even though Naruto himself was innocent. It could also be a case of false information being spread around the village which made his parents believe lies about him.
It could be that in this fanfiction, there are some external influences like an enemy who has manipulated Naruto's mind. The enemy might have planted false memories or ideas in Naruto's head, making him believe that his parents are not who he thought they were, leading to his rejection.
One possible reason could be that he discovers a dark secret about his family. Maybe he finds out that his parents were involved in something he can't accept, like a deal with a dangerous enemy. So, to avoid being associated with it, he runs away.
One possible reason could be that Naruto discovers some dark family secret that his parents want to keep hidden. For example, if there was a connection between the Uzumaki clan and some forbidden jutsu, and they fear Naruto might be exploited because of it. So they banish him to protect the clan's reputation and his own safety.