Another possibility is that there is a powerful and malevolent magical being that has a vendetta against Twilight. It realizes that it can't directly attack Twilight because of her strong magic, so it targets her friends. It uses mind - control or deception to make her friends betray her. This antagonist's goal could be to steal Twilight's magic or simply to destroy her reputation in the magical community.
It could be an outsider who manipulates Twilight's friends. This character might be envious of Twilight's popularity or power in the magical realm. They trick Twilight's friends into believing false things about her, making the friends turn against her.
It could be that an external force, like a dark wizard in disguise, is the main antagonist. This dark wizard targets Hermione because of her potential to be a great threat to their evil plans. They use magic to cloud the minds of her friends, making them believe Hermione is up to no good. The friends, being under this spell, betray Hermione without realizing they are being manipulated. The dark wizard then watches as Hermione struggles with this betrayal, all part of their grand scheme.
Another possibility is that one of Twilight's own insecurities or fears takes on a form and becomes the main antagonist. It drives her to betray her friends as it convinces her that the Mane 6 are not as good as she once thought.
Another possibility is that there is no single main antagonist. It could be a combination of misunderstandings, village politics, and personal issues within Kurenai herself that lead to her betraying Naruto. For instance, the village elders might be pressuring Kurenai to keep Naruto in check, and at the same time, Kurenai has her own doubts about Naruto's power which could be misconstrued as a reason to betray him.
It could be one of the harem members who has a hidden dark side. Maybe she's jealous of Naruto's closeness to others in the harem and decides to turn the rest against him, so she becomes the main antagonist.
Maybe it's a new character created specifically for the fanfiction. This character could be a powerful sorcerer who has the ability to manipulate people's minds. He targets Goku out of jealousy for his power and popularity. By using his mind - control powers, he makes everyone around Goku believe that he's a traitor, thus making himself the main antagonist.
It could be a new character introduced in the fanfiction. Maybe someone who has infiltrated the Order and wants to create chaos by turning them against Hermione. This person could be a spy from the Death Eaters or another dark - aligned group, with the goal of weakening the Order from within by making them lose one of their most intelligent and powerful members.
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.
It could be a jealous Fairy Tail member. Maybe someone who is envious of Naruto's unique powers and the attention he gets from some of the guild members. This person could start spreading lies about Naruto to turn the others against him.
It could be Sasuke. He has had his own dark journey and might turn against Naruto and Ino in this fanfiction. His newfound power and different ideals could make him see Naruto and Ino as threats to his goals.
In a 'Twilight Betrayed by Her Friends' fanfiction, it could be that Twilight's friends become jealous of her powers. They feel overshadowed by her abilities and knowledge. So they start to undermine her at every turn. For example, they might ruin her chances of getting a special magical promotion or getting into an exclusive magical study group. Twilight is heartbroken at first but then decides to prove herself without their support and in the process, she might find new friends who truly appreciate her for who she is.