It could be Dumbledore. He always had his own plans and secrets. Maybe Harry discovers that Dumbledore was using him all along for some greater purpose that involved sacrificing Harry's well - being. Another likely betrayer could be Ron. Ron had moments of jealousy in the original story. In this fanfiction, his jealousy could have grown to the point where he turned on Harry for his own gain or out of envy.
Cinder Fall could be a likely betrayer. She's already a villain in the original series, and in a fanfiction, she could pretend to be an ally to one of the RWBY members only to betray them at a crucial moment, perhaps leading them into a trap set by Salem.
It could be an enemy who has infiltrated his team disguised as a friend. For example, in a crossover with Fullmetal Alchemist, an alchemist with the ability to change appearance might pretend to be on Kakashi's side but then betray him.
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.
Another possibility is that it could be a new character introduced in the fanfiction. This new character could be someone who gains Harry's trust quickly but then betrays him for personal gain or because they are secretly working for an enemy. For example, a new student at Hogwarts who seems friendly at first but is actually a spy for a dark wizard.
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.
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.