It could be that Naruto's pursuit of power to protect the village takes a dark turn. He delves too deep into a dangerous form of jutsu or power source. This causes him to become unstable and a threat to those around him. His friends are forced to distance themselves from him for the safety of the village. Naruto, realizing what he has become, goes into self - exile. There, in a desolate place, he finally meets his end, all alone.
In this kind of fanfiction, one possible plot could be that Naruto loses all his friends due to some unforeseen and tragic events. Maybe he makes a great sacrifice to save the village, but in the process, he becomes estranged from everyone. His friends might misunderstand his actions, or he could be cursed in a way that drives people away. Eventually, he dies alone, with his heroic deeds forgotten by most.
Perhaps Naruto is framed for a crime he didn't commit. As a result, the villagers turn against him once again, just like in his childhood. His friends try to defend him at first, but as the evidence seems to stack up, they start to have doubts. Naruto, feeling betrayed, decides to leave the village. He wanders alone in the world, facing many hardships and enemies. In the end, he succumbs to his injuries or an enemy's attack, dying alone.