It could be a consequence of Naruto's own overuse of the Nine - Tails' chakra. Naruto has always been pushing his limits when it comes to using the Nine - Tails' power. If he overdid it in a crucial battle, it could have damaged his body beyond repair. Kakashi, as his former teacher and a trusted friend, would be the one to hold him as he passed away, mourning the loss of such a great hero.
Kakashi's reaction would be complex. He is a man who has lost many people in his life. But Naruto was special. He would hold Naruto tightly, his hands trembling slightly. He might try to use some of his own chakra to keep Naruto alive a little longer, but deep down he knows it's futile. His face would show a mixture of pain, regret, and love. He would remember all the times he trained Naruto, all the lessons he taught him, and how Naruto had surpassed all expectations.
Perhaps Naruto has just learned some dark secrets about his past, such as the truth about his parents' death. Discovering such painful truths could easily make him break down and seek comfort in Kakashi, who he looks up to as a mentor. Also, it could be that he's feeling lonely. Despite having friends, there are times when the weight of his responsibilities makes him feel isolated, and crying in Kakashi's arms is a way to let out those pent - up emotions.
It could be due to a misunderstanding. Kakashi might think that Naruto is getting involved with something dangerous or has some potential that he can't handle. So, in his warped way of thinking, he abandons Naruto to protect him from himself or from some unknown danger.
One possible plotline could be that Kakashi is in a life - threatening situation during a battle against a powerful enemy. Naruto, seeing no other way to save him, uses a powerful and self - sacrificing jutsu that costs him his life. Another plotline might involve Naruto making a deal with some dark force to save Kakashi, but the price is his own life. Or perhaps in a mission gone wrong, Naruto takes a fatal blow meant for Kakashi.
One reason could be that he saw Naruto's potential later on and realized he could have been much stronger if he had trained him earlier. For example, Naruto has a great deal of chakra and tenacity, and with proper training from Kakashi earlier, he might have reached new heights faster.
One possible plot reason could be for Naruto to experience a great loss that changes his character completely. Maybe it's part of a dark plot where the enemy is so powerful that they manage to kill Hinata right in front of Naruto. This would fuel his rage and determination to become even stronger and seek revenge. Another reason could be related to some sort of sacrifice. Hinata might sacrifice herself to save Naruto or someone else important, and Naruto has to deal with the guilt and grief of her death.
One reason could be Kakashi's Sharingan. It's a very powerful and somewhat spooky ability. Naruto might see it in action in a way that scares him. Maybe Kakashi uses it to subdue an enemy in a really intense way that makes Naruto realize how dangerous Kakashi can be.
One possible reason could be training. Maybe Kakashi's training methods are too harsh for Naruto. Naruto is eager to become stronger quickly, but Kakashi might be holding him back in Naruto's eyes. For example, Kakashi could be making Naruto do repetitive basic drills instead of teaching him more advanced jutsu right away.
Kakashi could be in a difficult situation where he has to make a choice between Naruto and another more pressing obligation. For example, he might be under orders from higher - ups in the village to focus on training a different group of ninjas. So, even though he may like Naruto, he has to reject him in order to fulfill his other duties.
One possible reason could be that Kakashi is preoccupied with other important matters in the village. Maybe he has some top - secret missions or tasks assigned by the Hokage that demand his full attention, leaving him with little time to focus on Naruto.