Well, a plot could involve Hermione being influenced by a powerful dark magic item. This item warps her mind and makes her see Harry as a threat to the wizarding world. So, she betrays him by revealing his secrets to his enemies. Or perhaps she gets jealous of Harry's popularity and power and that leads to her betrayal in a moment of weakness.
In some fanfiction ideas, Hermione could be forced to betray Harry due to a loyalty spell gone wrong. She might be bound to another character who has malicious intents towards Harry. This could lead to her revealing Harry's plans to the wrong people. Also, she could be blackmailed into betraying him. For example, if someone discovers a dark secret from her past and uses it to make her do their bidding against Harry.
A great plot could be that they discover they are twins later in their Hogwarts years. This revelation could cause a stir in the wizarding world. They might then start to explore their family history together, finding out secrets about their parents that were previously unknown. Maybe they find out that their parents had some special mission that they now need to continue as twins.
One idea could be that they are adopted by a powerful but reclusive wizard. This wizard has his own motives for taking them in, like using their potential for a grand magical plan. Another plot could be that they are adopted into different families at first and then reunite later, realizing they have a special bond that goes beyond blood relations. Maybe they discover that their adoption was part of a prophecy protection mechanism, to keep them safe from the dark forces that are after them.
Well, a plot could involve Edward being betrayed by a mentor figure. This person could have been guiding him in alchemy all along but has a hidden agenda. Maybe they want to use Edward's unique alchemical abilities for their own dark experiments. Or, in a different scenario, Edward could be betrayed by a love interest. She might pretend to love him while actually spying on him for an opposing force, stealing his secrets and leaving him heartbroken and in a difficult situation.
Another possibility is that Fleur, in a bid to gain more influence in the magical world, uses Hermione's research on some ancient magic without permission. When Hermione finds out, she realizes Fleur has been using her all along, and this is the ultimate betrayal. Hermione then has to find a way to expose Fleur's actions and clear her own name.
A third plot could be that their presence in Ravenclaw changes the overall perception of the house. Usually seen as more cerebral and less action - oriented, Harry and Hermione bring a sense of adventure. They might convince their Ravenclaw housemates to join them in more dangerous quests, like exploring the Forbidden Forest for a rare ingredient for a potion that could help in the fight against the Dark Arts.
One plot idea could be that Harry, Hermione and Susan team up to solve a new mystery at Hogwarts that the teachers are overlooking. For example, a series of strange disappearances of magical creatures from the Forbidden Forest. They use their combined skills in magic, Hermione's research abilities, Harry's courage and Susan's unique knowledge of certain spells to track down what's happening.
One idea could be that their son's soul - bond gives him unique magical abilities. For example, he might be able to communicate with magical creatures on a deeper level. Another plot point could be that the soul - bond makes him a target for dark forces, who want to use his power for their own gain. Or perhaps the soul - bond leads to him having prophetic dreams about the future of the wizarding world, which he then has to figure out how to prevent or encourage.
One interesting plot idea could be how they initially react to the betrothal. Maybe Hermione is more accepting as she sees it as a way to strengthen the wizarding world, while Harry is more hesitant. Another idea is how they deal with Ron's reaction, since he has feelings for Hermione. They might have to work through their friendship with Ron while also coming to terms with their new relationship status.
One plot idea could be the challenges they face in the wizarding world due to their unexpected pregnancy. Maybe there are speculations and gossips among the wizarding community. Another could be how they prepare for the arrival of the baby, like choosing a magical nursery and magical baby items. And a third idea might be how they deal with the reactions of their friends and family, some being supportive and others being skeptical.
One plot idea could be that they are forced into an unexpected union due to some magical circumstances. Maybe a dark magic spell backfires and binds them in a way that leads to Hermione becoming pregnant. Another could be a story set in an alternate universe where they are on the same side and fall in love over time, and the pregnancy is a result of their new - found relationship. It could explore how they deal with the reactions of their respective families and friends.