World War II storyline
- Sgt. Robert "Bobby" Shaftoe, a gung-ho, haiku-writing United States Marine Raider.
- Lawrence Pritchard Waterhouse, an American cryptographer/mathematician serving as an officer in the United States Navy, although he is known to wear an Army uniform if the situation calls for it.
- Günter Bischoff, a Kapitänleutnant in the Kriegsmarine, who commands a U-Boat for much of the story, and later takes command of a new, advanced submarine fueled with hydrogen peroxide.
- Rudolf "Rudy" von Hacklheber, a non-Nazi German mathematician and cryptographer, who spent time attending Princeton University, where he had a romantic relationship with Alan Turing and befriended Waterhouse. He seems to know more about the mysterious Societas Eruditorum than any non-member.
- Earl Comstock, a former Electrical Till Corp. executive and US Army officer, who eventually founds the NSA and becomes a key policy maker for US involvement in the Second Indochina War.
- Julieta Kivistik, a Finnish woman who assists some of the World War II characters when they find themselves stranded in Sweden, and who later gives birth to a baby boy (Günter Enoch Bobby Kivistik) whose paternity is uncertain.
- “Uncle” Otto Kivistik, Julieta's uncle, who runs a successful smuggling ring between neutral Sweden, Finland, and the USSR during World War II.
- Mary cCmndhd (pronounced "Skuhmithid" and anglicized as "Smith"), a member of a Qwghlmian immigrant community living in Australia, who catches the attention of Lawrence Waterhouse while he is stationed in Brisbane.
- Glory Altamira, a nursing student and Bobby Shaftoe's Filipina lover. She becomes a member of the Philippine resistance movement during the Japanese occupation. Mother of Douglas MacArthur Shaftoe.
Fictionalized versions of several historical figures appear in the World War II storyline:
- Alan Turing, the cryptographer and computer scientist, is a colleague and friend of Lawrence Waterhouse and sometime lover of Rudy von Hacklheber.
- Douglas MacArthur, the famed U.S. Army general, who takes a central role toward the end of the World War II timeline.
- Karl Dönitz, Großadmiral of the Kriegsmarine, is never actually seen as a character but issues orders to his U-Boats, including the one captained by Bischoff. Bischoff threatens to reveal information about hidden war gold unless Dönitz rescinds an order to sink his submarine.
- Hermann Göring, who appears extensively in the recollections of Rudy von Hacklheber as Rudy recounts how Göring tried recruiting him as a cryptographer for the Nazis: Rudy delivers an intentionally weakened system, reserving the full system for the use of the conspiracy among the characters to locate hidden gold.
- Future United States President Ronald Reagan is depicted during his wartime service as an officer in the U.S. Army Air Corps Public Relations branch's 1st Motion Picture Unit. He attempts to film an interview with the recuperating and morphine-addled Bobby Shaftoe, who spoils the production with his account of a giant lizard attack and his harsh criticism of General MacArthur.
- Admiral Isoroku Yamamoto's 1943 death at the hands of U.S. Army fighter aircraft during Operation Vengeance over Bougainville Island fills an entire chapter. During his fateful flight, the Commander-in-Chief of the Japanese Imperial Navy's Combined Fleet reflects upon the failures and hubris of his Imperial Army counterparts, who persistently underestimate the cunning and ferocity of their Allied opponents in the Pacific Theatre of Operations. As his damaged transport plane completes its terminal descent, Yamamoto realizes that all of the Japanese military codes have been broken, which explains why he is "on fire and hurtling through the jungle at a hundred miles per hour in a chair, closely pursued by tons of flaming junk."
- Albert Einstein brushes off a young Lawrence Waterhouse's request for advice. During his year of undergraduate study at Princeton, Waterhouse periodically wanders the halls of the Institute for Advanced Study, randomly asking mathematicians (whose names he never remembers) for advice on how to make intricate calculations for his "sprocket question," which is how he eventually meets Turing.
- Harvest, an early supercomputer built by IBM (known as "ETC" or "Electrical Till Corp." in the novel) for the National Security Agency for cryptanalysis. The fictionalized Harvest became operational in the early 1950s, under the supervision of Earl Comstock, while the actual system was installed in 1962.
The precise date of this storyline is not established, but the ages of characters, the technologies described, and certain date-specific references suggest that it is set in the late 1990s, at the time of the internet boom and the Asian financial crisis.
- Randall "Randy" Lawrence Waterhouse, eldest grandson of Lawrence and Mary Waterhouse (née cCmndhd) and an expert systems and network administrator with the Epiphyte(2) corporation.
- Avi Halaby, Randy's business partner in Epiphyte(2), of which he is the CEO. He is descended on his mother's side from New Mexican Crypto-Jews, which detail, while seemingly included as a pun, is explored further in The Baroque Cycle. Avi is obsessed with using technology to prevent future genocides, namely by creating a handbook of basic technology and defense practices.
- America "Amy" Shaftoe, Doug Shaftoe's daughter (and Bobby Shaftoe's granddaughter) who has moved from the U.S. to live with Doug in the Philippines, and who becomes Randy's love interest.
- Dr. Hubert Kepler, a.k.a. "The Dentist," predatory billionaire investment fund manager, Randy and Avi's business rival.
- Eberhard Föhr, a member of Epiphyte(2) and an expert in biometrics.
- John Cantrell, a member of Epiphyte(2), a libertarian who is an expert in cryptography and who wrote the fictional cryptography program Ordo.
- Tom Howard, a member of Epiphyte(2), a libertarian and firearms enthusiast who is an expert in large computer installations.
- Beryl Hagen, Chief Financial Officer of Epiphyte(2) and veteran of a dozen startups.
- Charlene, a liberal arts academic and Randy's girlfriend at the beginning of the novel, who later moves to New Haven, Connecticut, to live and work with Dr. G.E.B. (Günter Enoch Bobby) Kivistik.
- Andrew Loeb, a former friend and now Randy's enemy, a survivalist and neo-Luddite whose lawsuits destroyed Randy and Avi's first start-up, and who at the time of the novel works as a lawyer for Hubert Kepler. He is referred to by Randy as "Gollum," comparing him to that character in the novels of J. R. R. Tolkien.
- Goto Dengo, a lieutenant in the Imperial Japanese Army and a mining engineer involved in an Axis project to bury looted gold in the Philippines. In the present-day storyline, he is a semi-retired chief executive of a large Japanese construction company.
- Enoch Root, a mysterious, seemingly ageless former Catholic priest and physician, serving as a coast-watcher with the ANZACs during World War II, later a chaplain in the top-secret British-American "Unit 2702," and an important figure in the equally mysterious Societas Eruditorum. In the present-day storyline, Root is portrayed as having a passionate belief that cryptography is important for maintaining freedom. Root spent the 1950s working at the National Security Agency and has since been based mostly in the Philippines as a Catholic lay-worker while lately "gadding about trying to bring Internet stuff to China, but to Randy this just sounds like a cover story for something else." Root also appears in Stephenson's The Baroque Cycle, which is set between 1666 and 1714.
- Mr. Wing, a wartime northern Chinese slave of the Japanese in the Philippines, who went on to become a general in the Chinese army and later a senior official in the State Grid Corporation of China. Described by Enoch Root as a "wily survivor of many purges," Wing is the only other survivor besides Goto Dengo of the Japanese gold burial project, and he competes with Goto and Epiphyte(2) to recover the buried treasure. Although Root and Wing do not meet during the action of the novel, Randy reflects that "it is hard not to get the idea that Enoch Root and General Wing may have other reasons to be pissed off at each other."
- Douglas MacArthur Shaftoe (named after General Douglas MacArthur), Bobby Shaftoe's and Glory Altamira's son. He is introduced near the end of the World War II storyline as a toddler, when he meets his father, who tries to explain Shaftoe family heritage during the Liberation of Manila. In the modern-day storyline, Douglas is a retired U.S. Navy SEAL officer and U.S. Naval Academy graduate, who lives in the Philippines and operates Semper Marine, an underwater survey business with his daughter, Amy, conducting treasure hunts as a sideline.
- Dr. Günter Enoch Bobby "G.E.B." Kivistik is introduced in the modern storyline as a smug, Oxford-educated liberal-arts professor from Yale who recruits, and later seduces, Randy Waterhouse's girlfriend, Charlene. In the World War II storyline he is the unborn son of Julieta Kivistik and one of three possible fathers (hence his unusual name). He is a minor character in Cryptonomicon, but both his [impending] birth and his participation in Charlene's "War as Text" conference catalyze major plot developments.
- Mary cCmndhd Waterhouse, Randy's Australian-born, Qwghlmian grandmother and Lawrence's wife.