One possible reason in fanfiction could be that Naruto's parents had to make a huge sacrifice for the greater good of the village. They might have known that Naruto would be in danger if they stayed with him because of their status or the secrets they carried. So, they chose to abandon him, believing that the village would take care of him. However, things might not go as planned in the fanfiction, and Naruto could face many hardships as a result.
In some fanfictions, it could be due to his parents being on a dangerous mission. They might have been forced to leave Naruto in order to protect him from the enemies who were after them. Maybe they thought that by abandoning him, the enemies wouldn't be able to find him as easily. Another reason could be that they were under some sort of dark magic or curse that made them act against their will. This could lead to them leaving Naruto without any choice.
Maybe his parents are dealing with some internal conflicts or secrets. They could be involved in something dangerous or forbidden, and they think that by ignoring Naruto, they are keeping him safe from the consequences of their actions. It could also be that they are under some sort of spell or mind - control that makes them act as if they don't care about him.
It could be that there was a prophecy related to his sister that made the family think she was more important. For example, a prophecy that she would be the key to saving the village in the future. And in their short - sighted view, they abandoned Naruto to focus all their resources on her.
Well, a common storyline could be that Harry, after being abandoned by his parents, is discovered by a powerful but reclusive wizard. This wizard takes Harry under his wing and trains him to be extremely powerful in magic, much more so than in the original story. This could lead to Harry having a different set of friends and enemies. Another idea is that Harry is abandoned near a magical school in another country. He grows up there, learning a different type of magic. When he finally comes to Hogwarts, he has a clash of magical cultures. And yet another could be that Harry is found by a magical organization that experiments on abandoned magical children. He has to escape from there and then find his true identity and place in the wizarding world.
Well, sometimes in fanfiction, the author wants to explore the theme of loneliness. So they create a scenario where Naruto's friends abandon him because they are influenced by the village's elders. The elders might spread false rumors about Naruto to maintain their control. His friends, being young and naive, believe these rumors and turn their backs on Naruto, which then leads to Naruto's journey of self - discovery and growth in solitude.
One possible reason could be jealousy. Maybe his sister is jealous of Percy's special abilities or the attention he gets. Another reason might be that she is forced to abandon him due to some external threat or danger that she believes will harm her if she stays with Percy. Or perhaps she has been brainwashed into thinking that Percy is a bad influence or a danger to her.
One possible plotline could be Naruto growing up on his own, but then discovers some hidden secrets about his parents that change his perspective. Maybe he finds out they had no choice but to leave him. Another could be that Naruto, after feeling abandoned, decides to prove himself to the village in an even more extreme way, like taking on super dangerous missions at a young age.
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 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.
Well, perhaps in the fanfiction world, Naruto's parents discover some kind of 'dark power' within him that they fear might be uncontrollable. They think that banishing him is the only way to keep the village safe from this potential threat. This could be a power that is different from the Nine - Tails' chakra and seems extremely dangerous to them.
One possible plotline could be Naruto growing up feeling extremely lonely and trying to find ways to gain his parents' attention even though they're not around. He might start to excel in ninja training not just to prove himself to the village but also in the hope that his parents would be proud if they were there. Another could be Naruto having vivid dreams about his parents and then waking up to the harsh reality of their absence, which could fuel his determination to find out more about them and why they ignored him.