A plot might involve some sort of misunderstanding or false prophecy that leads Harry to believe he has to force Hermione into doing something. However, this is a departure from the positive and trusting relationship they have in the books. Another could be that an external evil force is controlling Harry to do this, but again, it's a very uncharacteristic and disturbing idea.
Well, it's a rather dark concept. One possible plot could be that in a dark, alternate universe, Harry is under some sort of dark magic influence which makes him act against Hermione's will. But this is very much against the essence of their characters in the original series.
One possible plot could be that a dark magic spell forces Hermione to be in close proximity to Dumbledore for protection. Maybe there's a curse that only Dumbledore can counter, and Hermione has to stay near him at all times, which is described as 'riding' in a very odd sense.
One possible plot could be that they disappear to a parallel magical dimension. In this dimension, they have to learn new forms of magic to survive and find their way back home. Maybe they encounter strange magical creatures that are unknown in their own world.
One possible plot could be the secrecy and the struggle to keep it hidden from their friends. Another might be the way they deal with the reactions of Ron and other close friends. It could also involve how they plan for the future with a baby on the way in a world full of magic and danger.
In some fanfictions, it could be a misunderstanding that spirals out of control. Hermione and Ron misinterpret one of Harry's actions. For instance, Harry might be trying to protect them in a secret way, but it looks like he's up to something bad. Their lack of trust then grows, and they end up betraying Harry, perhaps by not coming to his aid when he really needs them, which could have serious consequences for Harry.
Perhaps in this fanfiction, it's part of a bet or a challenge. Harry loses a bet to Hermione and has to be her slave for a certain period. This could lead to various comical situations as Harry tries to fulfill Hermione's often demanding tasks.
One possible plot could be that Ron and Hermione suspect Harry is involved in some dangerous secret magic that could put him in harm's way. So they spy on him to find out more and end up discovering it's all a big misunderstanding. Maybe Harry was just trying to surprise them with a new spell he learned.
One possible plot could be that Hermione does something that Harry perceives as a great betrayal, like perhaps siding with the Ministry when Harry believes they are corrupt. This could lead to a deep - seated hatred from Harry.
One possible plot could be that there is a powerful dark wizard who forces Harry into marriage as part of a grand scheme to gain control over the wizarding world. Maybe this wizard has some ancient magic that compels Harry and he has to find a way to break free while also dealing with the political and social ramifications of this forced union within the wizarding community.
One possible plot could be that Hermione accidentally casts a spell on Harry during one of their Hogwarts adventures, turning him into a pet. She then has to take care of him while trying to find a way to reverse the spell. Along the way, they encounter various challenges and have to rely on their friendship to get through.
One plot could be that Hermione tries to hide her crush from everyone, especially her friends. She's always been so focused on academics and helping Harry, and this newfound emotion throws her off balance. So she has to juggle her normal life while secretly dealing with her feelings. For example, she might accidentally get distracted in class because she's thinking about the person she has a crush on.