Thousands of years before the events in the novel, the planet's intellectuals entered concents (monastic communities) to protect their activities from the collapse of society.

The avout (intellectuals separated from Sæcular society) are banned from possessing or operating most advanced technology and are supervised by the Inquisition, which answers to the outside world.

The avout are normally allowed to communicate with people outside the walls of the concent only once every year, decade, century, or millennium, depending on the particular vows they have taken.

His teacher, Fraa Orolo, discovers that an alien spacecraft is orbiting Arbre – a fact that the world government (Sæcular Power) attempts to cover up.

The alien ship eventually declares its presence by shining a laser upon several Millenarian Maths (the bastions of those avout who have taken a thousand-year vow of isolation).

Shortly after that, the Sæcular Power summons many avout from Saunt Edhar, including Erasmas and a Millenarian named Fraa Jad.

After a dangerous journey over the planet's frozen pole, they reunite with Orolo at an archaeological excavation of Orithena, an ancient concent destroyed by volcanic eruption.

Erasmas travels to Saunt Tredegarh where he attends the Convox dedicated to dealing with the military, political, and technical issues raised by the existence of the alien ship in Arbre's orbit.

Research is conducted on the samples from Orithena, and the aliens are found to come from planets in four parallel and distinct cosmi: Urnud, Tro, Laterre and Fthos.

Through observation and experiment, Erasmas and his companions determine that the conference has been infiltrated by the aliens and unmask a French-speaking Laterran linguist named Jules Verne Durand.

Prior to launch and without their knowledge, the Sæcular Power implants each of them with miniaturized neutron bombs that will be used to kill everyone aboard the alien ship if the mission fails.

In the final narrative, Erasmas awakens in a hospital on the starship and learns that diplomatic negotiations are underway thanks to the successful destruction of the alien weapon.

Erasmas attends a diplomatic summit where a funeral ceremony is held for those lost on both sides and a peace process begins between the aliens and the Arbrans.

It is a set of rules governing what is (and is not) allowed for avout to know and/or do, and was codified centuries before the time of the story in the Second New Revised Book of Discipline.

Each of these celebrates "Apert", a festival opening the concent to the outside world and allowing the flow of information between them, on an interval determined by that number.

[2] Stephenson also cites as an influence the works of Kurt Gödel and Edmund Husserl, both of whom the character Durand mentions by name in the novel.

Paul Boutin wrote in The Wall Street Journal that "the lasting satisfaction of Anathem derives … from Mr. Stephenson's wry contempt for today's just-Google-it mindset.

"[7] On Salon.com, Andrew Leonard described the book as "a page turner and a philosophical argument, an adventure novel and an extended existential meditation, a physics lesson, sermon and ripping good yarn.

"[8] Michael Dirda of The Washington Post disagreed, remarking that "Anathem will certainly be admired for its intelligence, ambition, control and ingenuity", but describing it as "fundamentally unoriginal", "grandiose, overwrought and pretty damn dull.

"[10] The novel entered The New York Times Best Seller list for Hardcover Fiction at number one[11] and achieved the rare distinction for a novel of being reviewed in the scientific journal Nature.