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.
Perhaps the main antagonist is not a person but a concept or situation. The Order could be facing extreme pressure from the outside, like a new and powerful dark force emerging. In their panic and need to make quick decisions, they misjudge Hermione and betray her. So, in this case, the 'antagonist' is the fear and hasty decision - making within the Order that leads to Hermione's betrayal.
Obviously Hermione is one of the main characters. As for the others, it could include members of The Order such as Dumbledore, Sirius Black if he was still alive in the context of the story, and other Order members who are involved in the act of betrayal.
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 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 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.
Voldemort himself could be the main antagonist in this scenario. He might offer Hermione something she desperately wants in exchange for her betrayal. Maybe he promises to spare her Muggle - born friends if she gives up the Order's plans and secrets. His powerful and intimidating presence could easily force Hermione into a difficult situation where she feels she has no choice but to betray.
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.
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.
It could be Orochimaru. He's always been interested in Naruto and has his own devious plans. He might frame Naruto during the Chunin Exams to create chaos and further his own goals of obtaining power and knowledge. Orochimaru could use his henchmen or his jutsu to make it look like Naruto is involved in some sort of treachery.