An excerpt from Cryptonomicon was originally published in the short story collection Disco 2000, edited by Sarah Champion and published in 1998. Stephenson's subsequent work, a trio of novels dubbed The Baroque Cycle, provides part of the deep backstory to the characters and events featured in Cryptonomicon. Set in the late 17th and early 18th centuries, the novels feature ancestors of several characters in Cryptonomicon, as well as events and objects which affect the action of the later-set book. The subtext implies the existence of secret societies or conspiracies, and familial tendencies and groupings found within those darker worlds.
The short story "Jipi and the Paranoid Chip" takes place some time after the events of Cryptonomicon. In the story, the construction of the Crypt has triggered economic growth in Manila and Kinakuta, in which Goto Engineering, and Homa/Homer Goto, a Goto family heir, are involved. The IDTRO ("Black Chamber") is also mentioned.
Stephenson's 2019 novel, Fall; or, Dodge in Hell, a sequel to Reamde (2011), reveals that Fall, Reamde, Cryptonomicon and The Baroque Cycle are all set in the same fictional universe, with references to the Waterhouse, Shaftoe and Hacklheber families, as well as Societas Eruditorum and Epiphyte Corporation. Two "Wise" entities from The Baroque Cycle also appear in Fall, including Enoch Root.
Peter Thiel states in his book Zero to One that Cryptonomicon was required reading during the early days of PayPal.[7]
