Another possibility is that it's a character who has been in the background in the original story but now plays a major role in the fanfiction. For example, a character who has always had a secret admiration for Annabeth and through some unforeseen circumstances becomes the father.
There's a chance it could be a new character introduced in the fanfiction. Maybe someone who has a mysterious past and enters Annabeth's life briefly but leaves a big impact, resulting in her pregnancy.
In some fanfictions, it could be Gray. Their rivalry - turned - friendship has a lot of potential for such an unexpected plot twist where Gray is the father.
In some fanfiction scenarios, the father could be a character who was under a spell or some sort of mind - control when the encounter with Kiba happened. This would add an interesting twist to the story as Kiba has to deal with not only the pregnancy but also the mystery behind the father's identity and the circumstances of their encounter.
It could also be a new character introduced in the fanfiction. Maybe a powerful demigod from another camp who Annabeth meets during a diplomatic mission. This would create a whole new set of drama and conflict, as Annabeth would have to deal with her feelings for Percy and this new person, as well as the implications of having a child with someone other than Percy.
Most likely, Percy could be the father. They have a strong relationship in the original series, so it would be a natural choice. Their chemistry and shared adventures could be the basis for a story where they start a family together.
Maybe an antagonist who wants to disrupt the group dynamic. If Annabeth is a key part of a group, punching her could cause chaos and confusion among her friends. It could also be someone who has been influenced by dark magic or some sort of mind - control in the fanfiction. This would make them act against their normal nature and punch Annabeth without really having a personal grudge.
It could also be someone new, a character created specifically for the fanfiction. Maybe a powerful new demigod who catches Annabeth's eye, and their relationship leads to the pregnancy.
Her family could be a great help. If they are aware of the situation, they can step in. Maybe her parents can talk to the school authorities or even directly to the bullies' parents. Family support is always crucial in such situations.
It could be Michael. Since they have a complex relationship in the Roswell series, it's possible that their relationship takes a new turn and he is the father. Maybe they had a passionate night together that led to the pregnancy.
Maybe it's a human who has somehow discovered the world of demigods and is afraid of their existence. They shoot Annabeth out of fear and misunderstanding. Another option is that it's a rogue demigod who has gone bad and is working against their own kind. This character could have a personal grudge against Annabeth specifically, perhaps because of her intelligence and leadership skills which they envy.
It could be an enemy from the underworld. Maybe a powerful demon or a vengeful spirit that has a grudge against her. They might use their dark powers to harm her, like sending a bolt of dark energy her way.