Perhaps her main adversaries are a secret society within the wizarding world that has been operating in the shadows for centuries. This society might be made up of powerful and influential wizards who believe in a different order, one that involves subjugating non - pure - blood wizards. Hermione, with her Muggle - born status, is a prime target for them. They would try to undermine her at every turn, using their vast resources and political influence within the wizarding community. Hermione would have to fight not only their magic but also their attempts to smear her reputation.
The Akatsuki could still be the main villains. In a secret agent Naruto fanfic, they could be even more devious, using undercover agents of their own to disrupt the shinobi world while Naruto tries to stop their grand plan of collecting all the tailed beasts.
One possible plotline could be Hermione going undercover in a wizarding crime syndicate. She'd use her intelligence and magic skills to gather evidence and take them down. Another could be her being recruited by an international secret agent organization within the wizarding world to stop a dark magic weapon from being unleashed.
Harry and Ron could be her main allies. They've always been by her side in the original story, so it's likely they'd support her new adventure as a dragon rider. They could help her keep her dragon - riding activities a secret from the teachers at Hogwarts.
It could be a jealous wizard who was once in love with Hermione. Discovering she has a child with Fred, this wizard might seek to harm the child out of spite. He could use dark magic to try and kidnap the child or cause trouble for the family.
Well, Ron and Harry would most likely be main characters. They're Hermione's best friends, so they'd be right there by her side when she breaks her leg. They'd probably be the ones helping her get to the hospital wing, getting her books for her when she can't walk to the library, and generally just being there for her.
It could be a powerful wizard who has been in hiding all this time. Maybe someone with a dark past that the author wants to explore.
Another possible main opponent could be a power - hungry wizard within the Ministry of Magic. This wizard might be trying to implement unjust laws or gain more power at the expense of others. Hermione, with her strong sense of justice, would engage in a battle of wills to stop this wizard, using her knowledge, influence, and unwavering will to fight for what is right.
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.
Well, Snape is a rather strict and no - nonsense teacher. He might be initially shocked or appalled. He could give Hermione a stern lecture about focusing on proper academic work instead of fanfiction. Maybe he'd even deduct house points if he thought it was a waste of her time or inappropriate.
Another possibility is Harry Potter himself. This would be a very different take on their relationship. In some fanfiction, the strong bond between Hermione and Harry could be taken to a new level. Maybe in a situation where they are the last hope for the wizarding world, they conceive a child in secret to carry on some special magic or power that could save the wizarding community.