One idea could be exploring the backstories of the characters in more depth. Maybe showing how they came to be in the situation that led to the 'plague on both houses'.
The main theme could be about conflict and the futility of feuds. It might show how the actions of two opposing sides, symbolized by 'both your houses', lead to destruction and chaos, much like a plague that affects everyone involved.
I think the theme could be about the destructive nature of feuds and the toll they take on everyone involved. The plot might follow the characters' attempts to navigate and escape the chaos caused by the ongoing conflict between the two houses.
Another way to start is by introducing a new character or a new situation related to the 'plague on both houses'. For example, a mysterious traveler arrives at the time when the 'plague' is starting to spread. This traveler could have some knowledge or power that will either make the situation worse or better, and this can be the hook to start your fanfiction.
I'm not entirely sure as I haven't read this novel specifically, but typically in a story about two feuding 'houses', there would be leaders or representatives from each house as main characters. They would be the ones driving the conflict and making decisions that impact the situation.
One idea could be a story that focuses on the backstories of the minor characters. For example, exploring the life of a random student from one of the houses before they entered the academy. It could show their family, their dreams, and how they ended up at the academy.
One interesting idea could be how the different house traits blend. For example, the bravery of Gryffindor with the wisdom of Ravenclaw might create a new kind of heroic and intelligent character. Maybe in a houses merge fanfiction, students from different houses work together more closely than in the original series, leading to unique friendships and adventures.
One idea could be that the Plague Doctor arrives in the wizarding world during a mysterious illness outbreak. He might have unique magical remedies that are different from what the wizards are used to. Maybe he teams up with Harry Potter to find the source of the disease, which turns out to be a dark magic - created pathogen.
Well, in some fanfictions of 'they both die at the end', the focus might be on how they make the most of their last day. It could involve them doing things they were always too scared to do, like confessing their true feelings to someone. They might also try to right some wrongs from their past. For example, if they had a falling - out with a friend, they would reach out and make amends. And the beauty of it is that it shows the power of self - realization and growth even in the face of death.
Well, in some fanfictions, the fact that they are in different houses might lead to a situation where they are misunderstood by their housemates. For instance, Harry in Gryffindor might be suspected of being too close to Hermione from another house and vice versa. This misunderstanding could create drama and tension, which they then have to resolve while also dealing with the normal Hogwarts adventures like classes, Quidditch, and dealing with the likes of Malfoy.
A great plot for a three houses fanfic could be a what - if scenario. Like what if Edelgard never started the war? How would the relationships between the characters and the different houses develop? Or perhaps a fanfic where the teachers at the academy have to deal with a mysterious magical threat that is affecting the students. This could lead to new alliances between the houses as they work together to solve the problem.