The Gospel of the Flying Spaghetti Monster is a parody that spoofs Intelligent Design (ID) as a pseudo-science. The concept for the book originated from a letter written by the author, Bobby Henderson, in protest of the Kansas State Board of Education's decision to require intelligent design in their school science curricula as an alternative theory to natural evolution. With biting satire, Henderson surmises that evolution and ID can co-exist in the form of the supernatural and that our higher power is in fact a flying spaghetti monster (FSM). Henderson provides humorous and ludicrous scientific evidence to prove this theory. Those who believe in FSM are known as Pastafarians and try as much as possible to live like pirates, whose dwindling numbers have caused global warming. FSM Heaven includes a beer volcano and a stripper club, so the most easily-converted Pastafarians tend to be college men. The tongue-in-cheek Gospel contains many illustrations, flyers to help promote the religion, and papers and essays written by fictional experts who support the FSM theory with scientific or mathematical evidence.

The book is presented in three parts. The first, the "Blunders of Science," tears apart the concepts of both evolution and intelligent design theories and provides scientific explanations and other evidence for why FSM is the most credible theory. In the second part, "Explaining Pastafarianism," Henderson provides more details about FSM from its origination to present day, as well as more information on what it means to be a Pastafarian. The third section, "Propaganda," contains pamphlets to help market FSM, FSM craft projects and papers from members of the Enlightenment Institute, a fictitious think-tank dedicated to proving the existence of FSM.

With unrelenting satire, Henderson ultimately succeeds in conveying his belief that Intelligent Design is a pseudoscience conjured up by Christians pushing their Creationism agenda into public schools. His Gospel uses such pseudoscience tactics to show that a supernatural flying spaghetti monster is just as plausible as a Christian god (or any other) and that if Creationism is taught, then FSM should be included in the curriculum and given equal scientific credence.