The proposal had a preface. In this, Alan Moore explains the problems he has with the superhero genre. He criticizes crossover event with being marketing devices, forcing readers buy books they don't want to understand what is going on and forcing the books to take part said event. He said the superhero genre needed more definitive ends to their stories. As such, he intended the Twilight of the Superheroes to be basically a superhero Ragnarok and avoid these before-mentioned problems.
The story's framing device has future incarnations of Rip Hunter and John Constantine going to the past because of disaster in their time. Rip and John would appear in other comic and try to recruit or warn the main characters of those books. However, the creators of the the comics being published at the time would have the choice to participate or not.
The main narrative, which is told by the present and future John Constantine(s) talking to each other, is that in the future the world was controlled by superhero dynasties (such as the Superman and Wonder Woman's House of Steel, the Marvel Family's House of Thunder, an unnamed Teen Titan house, an unnamed Justice League house and a super villain alliance). However, Superboy and Mary Marvel Jr. wanted to get married. This act would have unite the House of Thunder and House of Steel thus destroying the status quo. Several characters, including Constantine, tried to stop this alliance. Batman form a cabal of non powered superheroes. The Green Lanterns, Thangarians and Martians form an alliance. The factions had a massive battle that killed most of the super-powered people. The story had a side story focusing on a superhero ghetto where old superheroes live.
In the framing device, it turned out Rip and John actually went back in time to cause the disaster, because it would free humanity from the tyrannical rule of the superhumans.