The gods are always a possibility. Zeus, for example, has been distrustful of Percy in the past. If Zeus feels that Percy is getting too powerful or is a threat to his rule, he could engineer a situation where Percy is betrayed. He might use other demigods or even mortals to turn against Percy.
One possible plot could be that Percy is betrayed by one of his closest friends in Camp Half - Blood. Maybe Annabeth turns on him out of jealousy over his growing powers or a misunderstanding. Percy, feeling deeply hurt, decides to disappear into the mortal world. He cuts off all ties with the demigod community and tries to live a normal life, but his past keeps haunting him as monsters still sense his presence.
In the 'Percy Jackson Disappears' fanfiction, perhaps Percy could be kidnapped by an unknown enemy. Maybe it's a new villain who has a vendetta against the demigods. This would lead to his friends, like Annabeth, going on a desperate search for him, facing many dangerous challenges along the way.
There's a chance that it could be a character from Percy's family. For example, a distant relative who has been corrupted by some dark magic. They might betray Percy for their own gain or because they are being controlled, and this betrayal could lead to Percy being killed.
A group of rogue demigods could be the main antagonists. They believe that Percy is too powerful and his presence is causing more problems than solutions in the demigod world. So they make him disappear. But when Percy comes back, he shows them that they were wrong and that they have been mislead by false beliefs.
Well, he might disappear because of a powerful curse from an ancient enemy. Maybe he gets trapped in a different dimension. When he returns, he could have new powers or knowledge. For example, he might have learned some secret magic from the other dimension that helps him defeat a new threat in the Percy Jackson world.
Apollo might be the betrayed god. He could have been tricked by another god into betraying Percy. For example, Apollo might have been promised more power or a higher status among the gods if he turned against Percy. But then he realizes too late that he's been used and that he's actually betrayed someone who could have been an ally.
The gods, especially Zeus. He has always been a bit suspicious of Percy. In fanfiction, he could easily be written as spreading lies about Percy to the other gods and demigods, leading to everyone turning against him. Also, some new characters introduced in fanfiction might be the ones who start the chain of events that lead to Percy's all - around betrayal.
One possible reason for Annabeth to betray Percy in fanfiction could be a misunderstanding. Maybe she was misled by false information about Percy's actions or intentions. For example, if someone spread rumors that Percy was secretly working against the demigods, Annabeth might believe it without getting the full story.
Another aspect could be that Percy is betrayed by a family member. For example, if it is revealed that a relative he trusted was working for an enemy all along. This would shatter Percy's world as family has always been important to him, and it would be a major plot point in the fanfiction, leading to his emotional and physical struggles.