Genesis Noir plays as a metaphorical narrative between a film noir-style detective movie and aspects of the creation and potential destruction of the universe. It plays out the events of the Big Bang as a metaphor between a broken romance between No Man (representing time) trying to stop Golden Boy (representing energy) from killing Miss Mass (the mass of the universe).
No Man, a watch maker, has fallen into depression after breaking up with Miss Mass, a night club singer. He tries calling her and hears her crying for help, and racing to her apartment finds that she is about to be shot by Golden Boy, the saxophone player from her band. After touching the spent bullet casing with a strange spiral marking, No Man finds he can pause time, and determines he can stop Golden Boy’s bullet by creating a black hole. He then proceeds to track down more of the spiral symbols through events that would occur without the black hole and turn them golden; these are told through various vignettes that follow the creation of the universe and stages of life on Earth to obtain these. Among these, No Man befriends the Huntress, the Ronin, the Musician, and the Scientist. Further, these vignettes reveal that Golden Boy has found his fame through Miss Mass, and became jealous of when No Man started a relationship with her.
Eventually collecting enough spirals, No Man converts their energy to create a black hole, but which begins consuming all of reality. A white figure, an amalgamation of the Huntress, Ronin, Musician, and Scientist, appears to comfort No Man, and shows him he can see all the possibilities in time, and that he does not have to save everyone. With this revelation, No Man returns to the point where he first had his encounter with Miss Mass, and forces himself to turn away, changing the timeline to allow Golden Boy kill Miss Mass, and allowing the universe to be created.