Besides referring to the Latin term for nothingness, Nil is also a phoneme of the protagonist, Proun Nul. Nul is employed by the city of Nihilopolis X (the city is rebuilt each time the people destroy the previous one) as a deconstruction engineer on board the Derrida (named for Jacques Derrida). The citizens of Nihilopolis are committed to the philosophical principle of nihilism, and Nul's job involves destroying ideas (manifested as large edifices in the desert) before they can infect the population. In keeping with Nil's motto "In Nothing We Trust", this constant work has led to a war with the neighboring republic of Optima.
After a conversation one night with his friend Mr. Ooze in the Gripe Pit bar, Nul begins to question the foundation his society is built on -- namely, nothing. The average Nilian has no conception of love save as selfish DNA, no higher aspiration (besides an elevator between Nil and Hell, Nil sports individuals whose workaholic existence leaves them no time to think about alternatives) in life, and no pleasure beyond the cynical moment. Suicide booths are placed throughout Nil for anyone to use when they're extremely depressed.
On the following day, Nul at his job has to get the engines of the Derrida to full power to destroy an idea edifice. One crew member, Mr. Sly, is burned alive, and it's known among his friends and co-workers that Sly and Nul resented each other. An investigation is started by the Hypocripope, the chief religious authority of Nil, who also happens to be Mr. Sly's uncle. When Nul is taken to be interrogated by two of Hell's demons, his words are twisted into a confession of guilt. Once in jail, Nul walks out unhampered by the police because the people of Nil have become so indoctrinated by the ruling ideology that no one ever tries to escape. The demons, not wanting to return to Hell, concoct a story that Nul broke out of jail and slew dozens of guards in his escape.
Nul takes a train to Borderville and intends to defect to Optima when he's intercepted by Jacob Proudsmear III, an art dealer who considers turning him in before Nul makes up the story that he's the leader of a Nilean terrorist group, The Bowel Movement, and that he can get Proudsmear "The Gum of Egoh Dadah" after Nil is overthrown. From Borderville, Nul rides on an ammunition truck toward No Man's Land and is drafted into the Nilean army. A chance meeting between himself and a paraplegic Optiman on the battlefield convinces Nul that Optima doesn't offer anything better -- or worse -- than Nil if he doesn't believe himself. When confronted by an Optiman Battleziggurat, Nul decides to go AWOL and return to Miss Void, the woman he loves back in Nil. Other members of his unit retreat as well, and Obliterator Plee joins Nul is returning to Nil.
The streets of Nihilopolis are deserted because the Hypocripope made a grand decision to relieve the problem of suffering: kill everyone. Nul arrives in his soldier's uniform as Miss Void's apartment and she's excited by what she heard about Nul as a terrorist. After some intense sexual activity, Nul leaves the apartment and proclaims, "I believe in love, I believe in beauty, I believe in truth and honesty and justice and the Tooth Fairy and the inner beauty of humanity!" A Nilean soldier overhears this statement and shoots Nul, liberating him from his "prison of the flesh".
Nul dies smiling, and the last scene of the novel has him relaxing on a beach with a photograph of Miss Void and the presence of Nah, a dream character that had appeared to Nul twice before as a Mayan glyph.
Nil is illustrated in black and white with many death motifs.