Another possibility is that it could be a corrupted version of one of Goku's closest friends. Let's say Vegeta gets corrupted by some dark power. In his corrupted state, he turns everyone against Goku. He uses his influence and his knowledge of Goku's weaknesses to make the others believe that Goku is a danger to them, making the corrupted Vegeta 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.
In some cases, it could be an ancient and evil magical being that has been awakened. This being has the ability to manipulate people's minds and convinces everyone that Harry is evil. It wants to isolate Harry before attacking him directly for some unknown but dark reason.
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 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.
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 a jealous rival. This rival might have always been envious of Percy's popularity and skills. So, they manipulate Percy's friends into betraying him to get Percy out of the way and take over his position.
It could be a new character, someone who is jealous of Naruto's growing power and popularity among the girls. This person might spread false information to turn everyone against Naruto. Maybe a rogue ninja who has infiltrated the village and has a vendetta against Naruto for some unknown reason.
The Ministry of Magic itself could be the main antagonist. They might be so afraid of Harry's growing power and influence that they create false evidence to make everyone believe he has betrayed the wizarding world. They try to control the situation by turning everyone against Harry.
The Ministry of Magic could be the main antagonist. They might be the ones who spread lies or misinformation about Harry, causing everyone to abandon him. They could be afraid of Harry's power or have some ulterior motives to get rid of him. They could use their influence and authority to turn the public against Harry, making his life a living hell as he tries to survive on his own.
Maybe a new, powerful and evil ninja from another land. This ninja could have come to the village and caused a lot of chaos, making Naruto believe that no one in his village was capable of protecting themselves or him. So he blames everyone for their weakness and starts to hate them all, with this new ninja being the root of the problem.
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.