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.
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.
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.
Perhaps she's a sister who was thought to be dead but actually survived. She could have been corrupted by the experiences she had while being 'dead'. When she returns, she blames Percy for not saving her properly. This false blame leads her to betray Percy. She could start spreading rumors about Percy being a coward or a bad leader among the demigod community.
Luke might be the one to betray Percy again in a fanfiction. Even if he had a change of heart before, perhaps in this fanfiction he's been influenced by some dark force once more. He could pretend to be on Percy's side and then stab him in the back when Percy least expects it.
Perhaps Percy's loved ones are made to believe false rumors about him spread by an unknown enemy. As a result, they turn their backs on him. Percy would need to find a way to expose the real culprit behind the rumors and regain the trust of his friends and family.
One character that could betray Percy is Thalia. She has her own issues with the gods and her place in the world. Maybe she gets jealous of Percy's growing popularity and power among the demigods. So, she decides to side with an enemy to take Percy down a notch. Additionally, some minor characters that Percy has helped in the past could be the ones to betray him. They might feel indebted to him but also resentful at the same time. An enemy could manipulate their feelings and turn them into traitors against Percy.
Ares could be a likely character. He's always been somewhat of a wild card in the Percy Jackson series. He might betray Percy for his own amusement or to gain more influence in Olympus. Another could be Zeus. He's often paranoid about his power and might see Percy as a threat and betray him to protect his throne.
It could be Ares. He might see the Twilight vampires as a new source of power or chaos. He manipulates Percy into believing that the Twilight characters are evil and need to be stopped. So Ares becomes the main antagonist as he's the one driving Percy to betray the Twilight group.