In a fanfiction like this, it could be that Percy's powers or abilities were starting to make others jealous. His friends might have felt overshadowed and, in a moment of weakness, turned on him. Also, there could be an outside influence, like a dark force that was manipulating people's minds to make them betray Percy.
Perhaps Percy had made a difficult decision that others didn't understand. He might have sacrificed something important for the greater good, but it was misinterpreted as a selfish act. For instance, he could have given up a chance at a great reward to save a group of strangers, but his friends thought he was being stupid and ungrateful to them for not sharing the opportunity, and so they betrayed him.
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.
Another possibility is that there is some kind of dark influence at work. A powerful and malevolent force could be manipulating people's minds to turn them against Ash. This force might see Ash as a threat and use this underhanded method to get rid of him, causing his world to crumble as he is betrayed by all.
In this kind of fanfiction, one way it could develop is that Minato might be under some kind of dark influence. Maybe an enemy has a powerful genjutsu that makes Minato see Naruto as a threat to the village instead of his son. This would lead to actions that Naruto perceives as betrayal. Naruto, being the strong - willed character he is, would likely be extremely confused and heartbroken at first. He would then probably try to find out the real reason behind Minato's actions, starting his own journey of discovery.
In some fanfictions, Tsunade might betray Naruto due to political pressure. Maybe the village elders force her hand, believing Naruto's power is too dangerous. It could also be a misunderstanding, like false information about Naruto being a threat to the village reaching Tsunade.
One way it could develop is if Dumbledore withholds important information from Hermione about her family or her own magical abilities. He might do this because he fears she will use that knowledge in a way that could disrupt his grand plan for the wizarding world. For instance, Hermione discovers she has a special power that could defeat Voldemort easily, but Dumbledore has kept it from her all along, making her feel extremely betrayed as she could have saved many lives if she knew earlier.
One possible way this could develop is through a misunderstanding. Maybe Naruto is framed for a crime he didn't commit, and his friends believe the false evidence against him. For example, an enemy could plant evidence that makes it seem like Naruto is working with the villains. His friends, not knowing the truth, turn their backs on him. This would lead to Naruto feeling extremely hurt and isolated, and he might have to go on a journey to prove his innocence on his own.
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.
Perhaps in the fanfiction, an evil version of Goku from an alternate timeline arrives. This impostor causes chaos and destruction, but everyone blames the real Goku. His family and friends are deceived by the look - alike. Goku tries to prove his innocence but no one will listen. He might have to find a way to expose the impostor and regain the trust of those he loves.
One way the plot could develop is that Naruto begins to trust the wrong people because he doesn't remember who he should trust. This could lead to him getting into dangerous situations. Meanwhile, his true friends are desperately searching for a way to reverse his memory loss. As the story progresses, Naruto might start to have flashes of his old memories, which would add some mystery and hope to the plot.
It could be a jealous rival. This rival might have always been envious of Percy's popularity and skills. So, they manipulate Percy's friends into betraying him to get Percy out of the way and take over his position.