I haven't actually read the 'End of Ever After' novel specifically, but generally, it could be about the conclusion of a long - held state of 'ever after' like the end of a happily - ever - after scenario in a fairy - tale - like world. It might deal with the breakdown of an idyllic situation, perhaps due to some external force, internal conflict, or the passage of time.
Well, Homestuck does have some characteristics of a visual novel. It presents a complex narrative with visual elements and user interaction. But it also has unique features that set it apart from traditional visual novels.
Since I don't have detailed knowledge of the 'after ever after novel', it could potentially be a fantasy novel where the heroes have saved the world from an evil force and now the story is about how the world is like in the aftermath. It might explore how the different species interact now that the threat is gone, how the political structure has changed, and how the individual characters grow and adapt to this new world. There could be new challenges that arise from the very solution that saved them in the first place, and the novel could be all about that exploration.
Since I haven't read the 'after ever after novel', the main characters could be a family. After a major upheaval in their lives, like the loss of a family member or a financial disaster, they each struggle in their own way. One might be a rebellious teen trying to break free from the new constraints, while another could be a parent trying to hold the family together. And there could be other characters around them who either help or hinder their journey in this 'after' phase.
First, you need to be really familiar with the Homestuck universe and its characters. Understand their personalities and the overall storylines. Then, come up with an interesting plot that fits within that world.