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.

Jerzy Rugby is trying to create truly intelligent robots. While his actual life crumbles, Rugby toils in his virtual office, testing the robots online. Then, something goes wrong and zillions of computer virus ants invade the net. Rugby is the man wanted for the crime. He's been set up to take a fall for a giant cyberconspiracy and he needs to figure out who — or what — is sabotaging the system in order to clear his name. Plunging deep into the virtual worlds of Antland of Fnoor to find some answers, Rugby confronts both electronic and all-too-real perils, facing death itself in a battle for his freedom.

Set in 2030–2031, ten years after the events of Software, Wetware focuses on the attempt of an Edgar Allan Poe-obsessed bopper named Berenice to populate Earth with a robot/human hybrid called a meatbop. Toward this end, she implants an embryo in a human woman living on the Moon (Della Taze, Cobb Anderson's niece) and then frames her for murder to force her to return to Earth. After only a few days, she gives birth to a boy named Manchile, who has been genetically programmed to carry bopper software in his brain (and in his sperm), and to grow to maturity in a matter of weeks.