It varies from one fanfiction to another. Some fanfictions might depict Naruto as dead to introduce a new set of challenges for the remaining characters. For example, if Naruto dies, Konoha might be left vulnerable, and characters like Sasuke or Sakura would have to step up in different ways. But there are also plenty of fanfictions where Naruto remains alive and continues his journey, perhaps facing new and even more dangerous threats than in the original series.
One consequence could be that it disturbs the balance of the ninja world. The dead are supposed to rest, and by controlling them, Naruto might be messing with the natural order. This could lead to other ninja clans or villages seeing him as a threat.
Kakashi could be another important character. As a mentor figure, he might be guiding the younger generation through the difficult times after Naruto's death, using his experience and wisdom to keep the village stable.
In some fanfics, it could be due to a forbidden jutsu he discovers. Maybe he stumbles upon an ancient scroll that details the process of controlling the dead.
In some fanfiction concepts, it could be due to a new, powerful jutsu he discovers or perhaps as a result of some ancient curse or blessing that is bestowed upon him.
It could be a rogue ninja from another village who has a vendetta against Naruto. This ninja might have set a very elaborate trap that made it seem like Naruto was killed and left his body in a place where his friends would find him and think he was dead.
Maybe it's his father, Minato. Minato has a lot of things to tell Naruto, like more about the Uzumaki clan and how to better use the power of the Nine - Tails. And as his father, their connection is very strong, so it's quite possible that he is among the first dead Naruto talks to.
Perhaps there was some sort of dark influence or mind - control at play. An enemy might have manipulated Kakashi's mind in such a way that he believed Naruto was a threat and thus left him for dead, not realizing his true self.
One possible reason could be a misunderstanding. Maybe they were misled by false information or an enemy's trickery that made them think Naruto was a threat at that moment. Another reason might be extreme pressure or a life - or - death situation where they thought sacrificing Naruto was the only way to save the rest of the team or complete a crucial mission.