The action takes place in two periods — World War II and the late 1990s, during the Internet boom and Asian financial crisis. In 1942, Lawrence Pritchard Waterhouse, a young United States Navy code breaker and mathematical genius, is assigned to the newly formed joint British and American Detachment 2702. This ultra-secret unit's role is to hide the fact that Allied intelligence has cracked the German Enigma code. The detachment stages events, often behind enemy lines, that provide alternative explanations for the Allied intelligence successes. United States Marine sergeant Bobby Shaftoe, a veteran of China and Guadalcanal, serves in unit 2702, carrying out Waterhouse's plans. At the same time, Japanese soldiers, including mining engineer Goto Dengo, an old friend of Shaftoe's, are assigned to build a mysterious bunker in the mountains in the Philippines as part of what turns out to be a literal suicide mission. Circa 1997, Randy Waterhouse (Lawrence's grandson) joins his old role-playing game companion Avi Halaby in a new startup, providing Pinoy-grams (inexpensive, non-real-time video messages) to migrant Filipinos via new fiber-optic cables. The Epiphyte Corporation uses this income stream to fund the creation of a data haven in the nearby fictional Sultanate of Kinakuta. Vietnam veteran Doug Shaftoe, the son of Bobby Shaftoe, and his daughter Amy do the undersea surveying for the cables and engineering work on the haven is overseen by Goto Furudenendu, heir-apparent to Goto Engineering. Complications arise as figures from the past reappear seeking gold or revenge.

In his youth, Richard “Dodge” Forthrast founded Corporation 9592, a gaming company that made him a multibillionaire. Now in his middle years, Dodge appreciates his comfortable, unencumbered life, managing his myriad business interests, and spending time with his beloved niece Zula and her young daughter, Sophia. One beautiful autumn day, while he undergoes a routine medical procedure, something goes irrevocably wrong. Dodge is pronounced brain dead and put on life support, leaving his stunned family and close friends with difficult decisions. Long ago, when a much younger Dodge drew up his will, he directed that his body be given to a cryonics company now owned by enigmatic tech entrepreneur Elmo Shepherd. Legally bound to follow the directive despite their misgivings, Dodge’s family has his brain scanned and its data structures uploaded and stored in the cloud, until it can eventually be revived.

There's no way William A. Cozzano can lose the upcoming presidential election. He's a likable midwestern governor with one insidious advantage - an advantage provided by a shadowy group of backers. A biochip implanted in his head hardwires him to a computerized polling system. The mood of the electorate is channeled directly into his brain. Forget issues. Forget policy. Cozzano is more than the perfect candidate. He's a special effect.

The story, set in the present day, centers on the plight of a hostage and the ensuing efforts of family and new acquaintances, many of them associated with a fictional MMORPG, to rescue her as her various captors drag her about the globe. Topics covered range from online activities including gold farming and social networking to the criminal methods of the Russian mafia and Islamic terrorists.

At the beginning of the novel, the main character, Hiro Protagonist, discovers the name of a new pseudo-narcotic, "Snow Crash", being offered at an exclusive Metaverse nightclub. Hiro's friend and fellow hacker Da5id falls victim to Snow Crash's effects, which are apparently unique in that they are experienced in the Metaverse and also in the physical world. Hiro uses his computer hacking, sharp cognitive skills, and sword-fighting to uncover the mystery of "Snow Crash"; his pursuit takes the reader on a tour of the Sumerian culture, a fully instantiated anarcho-capitalist society, and a virtual meta-society patronized by financial, social, and intellectual elites. As the nature of Snow Crash is uncovered, Hiro finds that self-replicating strings of information can affect objects in a uniform manner even though they may be broadcast via diverse media, a realization that reinforces his chosen path in life.

The protagonist in the story is Nell, a thete (or person without a tribe; equivalent to the lowest working class) living in the Leased Territories, a lowland slum belt on the artificial, diamondoid island of New Chusan, located offshore from the mouth of the Yangtze River, northwest of Shanghai. At the age of four, Nell receives a stolen copy of an interactive book, Young Lady's Illustrated Primer: a Propædeutic Enchiridion, in which is told the tale of Princess Nell and her various friends, kin, associates, &c., originally intended for the wealthy Neo-Victorian "Equity Lord" Chung-Sik Finkle-McGraw's granddaughter. The story follows Nell's development under the tutelage of the Primer, and to a lesser degree, the lives of Elizabeth and Fiona, girls who receive similar books. The Primer is intended to steer its reader intellectually toward a more interesting life, as defined by "Equity Lord" Alexander Chung-Sik Finkle-McGraw, and growing up to be an effective member of society. The most important quality to achieving an "interesting life" is deemed to be a subversive attitude towards the status quo. The Primer is designed to react to its owners' environment and teach them what they need to know to survive and develop.