The story is told in
vignettes that reflect Johnny's disjointed mental state. Vasquez leaves unexplained which events in the story are objective and which are subjective, and provides no
backstory about Johnny's origins. The series begins when a boy named Todd (later nicknamed Squee by Johnny, for the noises he makes when scared) wakes in the middle of the night to find Johnny in the bathroom of his family's new house. After a confrontation with Squee's
teddy bear, Shmee, Johnny leaves, informing Squee that they are neighbors. Later, Johnny goes on a rampage with a
spork in a "
Taco Hell" restaurant, incited by an elderly patron referring to him as "wacky". Following the slaughter, Johnny watches its coverage on the news. Later, Johnny captures and kills a patient and calm man named Edgar Vargas after discussing about the philosophy of murder with him, as well as explaining his mysterious need to collect blood to paint a wall in his house, and later kills a beautiful woman after contemplating over their "internal ugliness". He goes on a date with Devi, a cashier, and has a mental breakdown where he attempts to stab and kill her when he gives into his fear of losing his happiness, but Devi brutally beats Johnny and escapes. Sometime afterward, he kills everyone in his least favorite coffee shop, and kills a convenience store clerk over the inability to purchase a slushee. Johnny realizes there may be a supernatural force preventing him from being brought to justice for his murders. He and the sentient floating head "Nailbunny" journey through the seemingly endless basement of his house and discuss the nature of Johnny's psychosis, realizing the various forces at play with his mind. Johnny alludes to the mysterious evil force kept behind a wall, which needs to be kept from escaping through continuously repainting the wall with the fresh blood of his victims, as the urges of Eff Boy, one of two Doughboys who are psychically empowered by the entity behind the wall, and who wishes to keep it from escaping so that it cannot reclaim him. This is contrasted by Psycho-Doughboy, who urges Johnny to kill himself so that the seal will break, releasing his "master" from behind the wall. While journeying through the underground of his home, Johnny kills a cockroach named Mr. Samsa (after
Gregor Samsa, the main character of
Franz Kafka's short story
The Metamorphosis). Johnny also rigs a robotic arm and handgun to shoot him if he were to answer the phone if someone calls, further flaunting his belief in his own immortality. When Devi calls him on the advice of a friend (as seen in an earlier scene), Johnny answers out of curiosity and is shot in the head immediately after resolving not to kill himself. Around this time, a pair of his victims escape from the bloody wall as a formless monstrosity breaks free, and reality itself seems to be erased. Eventually, Johnny's soul arrives in
Heaven, where he meets
St. Peter, who becomes physically ill with all that Johnny has done throughout his life. With him distracted, Johnny enters Heaven and meets a demon woman named Damned Elise, who gives Johnny a tour. Johnny starts a massive psychic battle when he discovers that the souls in Heaven are immortal and have mental powers which includes the ability to explode people's heads. Later on in the tour, Johnny is brought before
God, who is a lazy, obese man sitting in a chair in a state of exhaustion. Johnny starts a tirade that ends with Elise sending him to
Hell. Johnny meets
Señor Diablo, who gives Johnny a tour of the underworld and reveals that Johnny is a "flusher" or "waste lock", a creature chosen to concentrate the spiritual byproducts generated by humans into a specific object or point in space, in this case the wall in Johnny's house. As Johnny died, the wall unleashed the built-up negative energy, in the process destroying the universe, which was then restored. Johnny instantly despises Hell as he interacts with the obsessively negative and selfish citizens, and is sent back to life by Señor Diablo. Later on Earth, Johnny is unsure if he really died or if he experienced some kind of hallucination, and he resolves to become emotionless in order to retain his control over himself. When a
copycat killer named "Jimmy" pays Johnny a visit and confesses to several murders and a rape, Johnny eviscerates him out of pure disgust. Afterward, Johnny visits Squee and tells him that he should look out for himself, otherwise he may become as mentally damaged as Johnny himself. The series ends with Johnny sitting on a cliff overlooking the city, writing in his diary, with the hopes that he will be "as cold as the moonlight" that touches the diary's pages. ==Filler strips==