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.
Without having read the 'A Plague on Both Your Houses' novel, we can only make educated guesses. In a story centered around two feuding houses, there may be characters who are the catalysts for the conflict. Maybe there is an ambitious member of one house who wants to gain more power at the expense of the other. And in the other house, there could be a character who is determined to defend their family's honor at all costs. There might also be characters who are more neutral, such as servants or outsiders who see the futility of the feud and try to mediate, but often get caught in the crossfire.
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.
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'.
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.
The two dogs are the main characters.
There might be a military leader who has to make tough decisions between fighting the war and dealing with the plague situation. Maybe there's also a civilian character who becomes an unlikely hero, helping others to survive the twin disasters of war and plague. It could also have an antagonist, perhaps someone who is spreading the plague deliberately for some malicious purpose.
The two main characters are the dogs. I can't recall their exact names at the moment, but they are the ones who are on the run throughout the story.
Without knowing the exact graphic novel, we can only speculate. There could be a young orphan as a main character, who has to fend for himself during the plague. Or perhaps a local leader who is responsible for making difficult decisions during the epidemic, like whether to quarantine the town or not. And there could be a wandering storyteller who records the events of the plague as they unfold.
Since I don't know the specific 'bottle houses novel', I can't say for sure. But it could be the builder of the bottle house as a main character.
I don't know as I haven't read the novel.