One possible plotline could be Naruto finding unexpected allies during his time left for dead. Maybe some characters who previously had no connection to him come to his aid out of a newfound sense of justice or a change of heart.
Another plotline could involve Naruto's inner struggle and growth while in this dire situation. He might discover new powers or a deeper understanding of his ninja way as he fights to survive. He could also have visions or encounters with past mentors in his mind, guiding him through this tough time.
Perhaps there's a plotline where Naruto's enemies think he's dead but he secretly starts to build an underground resistance. He uses his wits and the skills he has to slowly undermine his enemies' plans while they are off - guard, believing him to be gone for good.
Another plotline might involve Naruto's inner struggle and growth. He could discover new powers or a deeper understanding of his ninja way while on the verge of death. He might have to rely solely on his wits and the training he's had in the past to survive. For example, he could use his shadow clones in more creative and strategic ways to defend himself and find a way back to his village.
A plotline could involve a witch from the Left 4 Dead universe being summoned to the Naruto world. This causes chaos as the characters in Naruto have no idea how to deal with this strange new entity. They have to figure out her powers and how to stop her from causing too much destruction. At the same time, some of the Naruto characters might get dragged into the Left 4 Dead world in the process of trying to stop her. There, they team up with the survivors in that world to fight against the hordes of zombies and other witches.
One possible plotline could be that Hermione was attacked by a group of dark wizards while on a solo mission. They might have been after some knowledge she possessed. After the attack, she could be found by a mysterious figure who nurses her back to health and together they seek revenge.
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.
One possible plotline could be Naruto's struggle with abandonment issues. Since Kushina left, Naruto might have a harder time finding his place in the village. He could become more withdrawn and have to fight even harder to prove himself. Another could be the search for Kushina. Naruto might embark on a journey to find out why she left and try to bring her back.
Iruka Sensei could also be a candidate. He was one of Naruto's first supporters and has a deep connection with him. He would probably risk a lot to save Naruto.
He might survive through his own sheer willpower. Naruto has always been a tenacious character. So, even when left for dead, his determination to live and achieve his dreams could keep him alive against all odds.
In certain 'harry is dead fanfiction' stories, a plotline could be the new generation of wizards rising up in the wake of Harry's death. His death could be a catalyst for change. Younger characters who were inspired by Harry might form a new resistance against any emerging threats. They would have to learn from Harry's example and find their own strength to protect the wizarding world.
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.
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.