It might be that Hermione has a change of ideology. She could start to believe that the methods of the Order are wrong and that by betraying them, she can bring about a better solution to the wizarding world's problems. For example, she might think that the Order's fight against Voldemort is causing too much collateral damage and decides to side with another group she thinks can handle things more peacefully, though this would be a very controversial view within the context of the original story.
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.
One possible plot could be that Hermione is under the influence of a powerful and dark magical object or spell. This object or spell could cloud her judgment and make her act against the Order. It could be something she stumbles upon during her research, not realizing its true and dangerous nature at first. The fanfiction could then explore how she deals with the consequences of her actions once she realizes what she has done.
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 a member of the Order, out of jealousy or a wrong perception of Hermione's power, convinces the others that she is a liability. So, they betray her by not believing in her when she discovers something important or by preventing her from using her skills to help. Hermione, being the strong - willed character she is, would then strive to prove them wrong and expose the real issues within the Order.
One plotline could be that Ron is lured by the promise of power. He betrays Hermione to join a dark wizard or group that offers him something he desires, like more status in the wizarding world. Another could be a love triangle gone wrong. If there's a new character who Ron fancies and this person convinces him that Hermione is standing in the way of their relationship, he might betray her.
She might get revenge because she felt the Order made a decision that put her or her friends in danger. For example, if they sent Harry on a dangerous mission without proper support, Hermione could plan some elaborate scheme to teach them a lesson. Maybe she'd use her intelligence to expose some of their secrets or weaknesses.
One possibility could be that Hermione feels extremely betrayed and isolated. She might then turn to her own studies even more intensively, using magic to create a safe space for herself. Maybe she discovers some long - forgotten magic that could help her in this difficult situation.
One possibility could be that Misato betrays Shinji in the context of a mission. Maybe she has been influenced by some external force, like a secret organization within Nerv. She might sacrifice Shinji's safety for what she believes is the greater good of humanity, but Shinji sees it as a betrayal.
It could also be a misunderstanding. Hinata might be framed as a traitor. Some false evidence could be planted that makes Naruto and his friends believe she has betrayed them. This would lead to a lot of drama and conflict in the fanfiction as Naruto struggles with whether to believe Hinata or the evidence against her.
Well, it could be that Wonder Woman is somehow influenced by a powerful enemy or a mind - controlling device. Maybe she's forced to turn against Batman to protect something she values more, like her own people on Themyscira. Or perhaps there's a misunderstanding between her and Batman, and she misinterprets his actions as a threat to the world.
In this fanfiction, perhaps Percy is influenced by some dark force. This force convinces him that the Olympians are corrupt and need to be overthrown. He then betrays them by stealing important artifacts from Olympus that are crucial for its protection. He might also try to turn the demigods against the Olympians.
One possible plot could be that the Weasleys might betray Hermione over a powerful magical artifact. Maybe they believe she has become too power - hungry in her pursuit of knowledge about it and they side with those who want to keep it away from her.