Another possibility is that it could be a character who has been corrupted by dark magic. This character was once a friend or at least an acquaintance of the dragon rider. But the dark magic makes them see the dragon rider as a target. They betray the rider in the hopes of getting some sort of power or reward from a more powerful evil entity.
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.
It could be a jealous demigod. Maybe someone who is envious of Percy's popularity and Nico's unique powers. This person might see an opportunity to get rid of them and take their place in the demigod hierarchy.
Well, perhaps in the fanfiction, the dragon rider is betrayed when they are blamed for a crime they didn't commit. Maybe it was a theft of a powerful magical item. The real culprit sets up the dragon rider, and Percy, believing the false evidence, turns his back on the rider. The rider then discovers the real thief's identity and has to fight against both the false accusations and the real villain to clear their name and reconcile with Percy.
It could be his friend, like Mitsuki. Mitsuki has his own secrets and goals, and in some fanfiction, he might be forced to betray Boruto for the sake of some greater good in his mind. For instance, if he has to choose between following Orochimaru's orders and staying loyal to Boruto.
In some versions, it could be an evil version of one of Tails' friends. Maybe through some dark magic or experiment gone wrong, Sonic or another friend turns against Tails. Their altered state makes them see Tails as an enemy, and they start to undermine him and try to harm him, which would be a huge betrayal for Tails.
It could be Luke. Even in a time - travel scenario, Luke's bitterness towards the gods might lead him to betray Percy. He could use time - travel to his advantage, perhaps making deals with past versions of enemies to stop Percy from achieving something that would benefit the gods.
It could be Valerie. She has had a somewhat rocky relationship with Danny in the original series. In a fanfiction about betrayal, she might be pushed over the edge by jealousy or a misunderstanding about Danny's powers and his intentions. She could then use her ghost - hunting skills against Danny in a more malicious way than before.
A new character could be introduced as the betrayer. This character could be a fellow robot created by the same technology as Mega Man but with a corrupted program. This character could pretend to be on Mega Man's side, gain his trust, and then stab him in the back when he least expects it.
It could be Sakura. Maybe she becomes envious of Naruto's newfound godlike status. She might feel that he has changed too much and is no longer the Naruto she knew. So, she could side with those who want to bring Naruto down, either out of jealousy or a misguided sense of what's right for the village.
A love interest is also a common choice. In fanfictions, love can be a complicated and often treacherous thing. The love interest could have their own motives, like being forced by an external power or having a hidden agenda that conflicts with Fem Robin's goals.