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.
A new and powerful dark wizard or witch created specifically for the fanfiction could be the main antagonist. This character could have some sort of connection to Hermione's past or her family, and use that knowledge to force her to turn against the Order. They could be extremely cunning and have abilities that even the Order finds difficult to counter, making Hermione's situation even more desperate.
It could be a new villain that we haven't seen in the original Marvel universe. This villain might be able to manipulate Natasha's emotions and loyalty, making her betray Tony. For example, a powerful sorcerer who uses dark magic to control her.
In such a fanfiction, perhaps Hermione could be blackmailed into betraying the Order. Maybe an enemy discovers a deep secret about her family and forces her to give up Order secrets.
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.
The Konoha elders could be the main antagonists. They are often shown to be quite traditional and set in their ways in the original series. If Naruto goes against their old - fashioned ideas about the village's future and ninja code, they would likely oppose him strongly and could be the driving force behind making Naruto an outcast, which in turn could lead to his 'betrayal'.
If Rias betrays Naruto, she herself could potentially be the main antagonist. Since Naruto is usually seen as a protagonist, Rias' actions of betrayal would put her in direct opposition to him. Her motives and actions would then drive the conflict in the story.
Another possibility is a dark wizard or a group of dark wizards who are after some powerful magic that the Lestrange family has, and Hermione gets in their way as she tries to protect the family or uncover the secrets. They would be the main force that Hermione has to face and overcome throughout the fanfiction.
Perhaps a powerful magical being from a different realm is the antagonist. This being might mistake Hermione for someone else or see her as a key to something in the wizarding world. So, it uses its magic to make her disappear. This being would be very difficult to defeat or negotiate with, making it a huge challenge for those trying to find Hermione.
Well, if Misato betrays Shinji, she could herself become the main antagonist, at least from Shinji's perspective. Her actions of betrayal would put her in direct opposition to Shinji's goals and well - being.
It could be Lex Luthor. He's always looking for ways to take down superheroes. He might manipulate Wonder Woman into believing Batman is a threat, so she betrays him. Luthor is smart enough to create a complex scheme to drive a wedge between them.
It could be a power - hungry student who wants to undermine Hermione and Favo Prefect. This student might be jealous of their status as prefects and the respect they get from teachers and students alike. So, they try to create problems for them, like spreading false rumors or sabotaging their projects.