Hard-Boiled Wonderland and the End of the World alternates between two plots: one in the odd-numbered chapters and the other in the even-numbered chapters. It is eventually revealed that the unnamed first-person narrators in these plots are different parts of the same character’s consciousness.

Odd-numbered chapters are the hard-boiled chapters where the plot follows some conventions of detective fiction. Chapter 1 opens with the narrator in an elevator on his way to a job encoding and couriering data (Calcutec) in Tokyo. As the elevator slowly moves, he counts the change in his pockets, doing the math simultaneously, that is, using the right side of his brain for his right pocket and the left side of brain for the left pocket. He thinks he’s being watched and does a second count, arriving at a different sum. The narrator begins a third count of the change in his pockets, but the elevator doors open before he finishes.

A young woman dressed all in pink leads him through a corridor with oddly numbered rooms. He notes the sound seems off and she only mouths words—later it is revealed that the young woman’s grandfather has muted her with sound-dampening technology. The narrator notes the woman is curvy and thinks about his confusing attraction to curvy women.