Well, perhaps in this fanfic, the village elders could be behind the betrayal. They might frame Naruto for a crime he didn't commit to protect their own interests. His friends, being influenced by the elders' authority, would then turn their backs on him. Naruto would be forced to go on the run, constantly hunted by those he once considered family. He would have to find a way to clear his name and expose the real villains all while dealing with the emotional pain of the betrayal.
In such a fanfic, the plot might start with Naruto's friends gradually turning against him due to false rumors spread by a hidden enemy. They could start to exclude him from missions and isolate him within the village. For example, Sasuke might believe the lies and challenge Naruto, thinking he has changed for the worse. This would lead to a series of battles where Naruto has to fight not only his former friends but also his own feelings of betrayal and confusion.
One possible plot is that an unknown force uses a powerful genjutsu on the entire village, making everyone see Naruto as a threat. His friends, like Sakura and Kakashi, are not immune to this genjutsu. As a result, they start to attack Naruto. Naruto, being the kind - hearted person he is, doesn't want to fight back at first. But as the attacks become more and more intense, he realizes he has no choice but to defend himself while trying to figure out a way to break the genjutsu and restore his relationships.
One way this could develop is if Naruto's identity as the Jinchuriki of the Nine - Tails is fully exploited against him. People might fear his power and turn on him. For example, the village elders could spread false rumors about him losing control of the Nine - Tails, causing the villagers to shun him. Another possibility is that a powerful enemy uses mind - control or deception to make those close to Naruto, like Sakura or Kakashi, turn against him. This would be a huge blow to Naruto as he values his relationships deeply.
The main antagonist might be an organization that wants to take over the Hidden Leaf Village. They see Naruto as a major obstacle because of his strength and influence among the villagers. So, they devise a plan to make everyone in the village betray Naruto. They use mind - control techniques or spread misinformation on a large scale to achieve their goal. This way, they can weaken the village from within before making their move to take it over.
Well, one possibility is that Naruto is framed for a serious crime he didn't commit. Maybe someone fakes evidence that he's been working with the enemies of the village. His friends, believing the false evidence, turn their backs on him. He then has to fight not only against the village's distrust but also to clear his name and find out who really set him up.
In a Naruto betrayed by everyone harem fanfiction, the plot might start with Naruto being framed for a major crime against the village. The harem elements could be that his so - called harem members, who are usually his friends and admirers, are caught in a dilemma. They love Naruto but the evidence against him seems overwhelming. As the story unfolds, Naruto may have to fight not only to clear his name but also to win back the trust of his harem. It could involve him going on a journey to find the real culprit while facing the animosity of his former friends and the village he once loved.
In the fanfiction, it might be that Tsunade believes Naruto has become too dangerous. Maybe she's misled by false information about Naruto's new powers being uncontrollable and a threat to the village. So she decides to betray him to protect Konoha from a potential disaster.
It could be the very villagers who once looked up to Naruto. Their betrayal could turn them into antagonists as they might try to further harm Naruto to protect their own interests.
Maybe the gods are jealous of Naruto's ability to inspire people. In this fanfic, they could use their divine powers to make it seem like Naruto has committed heinous crimes. His village would turn on him, and he'd be on the run. Along the way, he might discover some ancient power that can counter the gods' treachery and use it to clear his name and get revenge on those who wronged him.
One possible plot could be that Tsunade is misled by false information about Naruto. Maybe some powerful enemy fabricates evidence that Naruto is a threat to the village. Tsunade, believing this, exiles Naruto. Naruto, feeling betrayed, then has to prove his innocence while also facing external threats.
One possible plot could be that Kushina is somehow influenced by an evil force. This force makes her believe false things about Naruto, like he's a threat to the village in the future. So, she betrays him by revealing his secrets or trying to harm him. Maybe she spreads lies about him which turns the villagers against Naruto even more.
Perhaps in this fanfic, Naruto is forced to make a choice between his ninja values and the Jedi code. He might choose something that the Jedi don't agree with, like using his chakra in a way that goes against their light - side - only beliefs. The Jedi then shun him, making Naruto feel betrayed. He might then try to find his own path, separate from both the ninja world and the Jedi order.