As with Neuromancer and later Gibson works, there are multiple story-line threads which eventually intertwine:
Thread One : In the southwestern USA, Turner, a corporate mercenary soldier, has been hired by former partner Conroy to help Christopher Mitchell, a brilliant researcher and bio-hacker, make an illegal career move from Maas' corporate fortress built into a mesa in the Arizona desert to Hosaka, a rival corporation. The attempt is a disaster, and Turner ends up escaping with the scientist's young daughter, Angie Mitchell instead. She carries the plans, implanted in her brain by her father, of the secrets of construction of the extremely valuable "biosoft" that has made Maas so influential and powerful. This "biosoft" is what multibillionaire Josef Virek (see thread three) desires above all else, so that he can make an evolutionary jump to something resembling omniscience and immortality. During their flight from both Maas and Hosaka agents, Turner and Angie stay with Rudy, the former's estranged brother, and Sally, his partner and caretaker. Rudy identifies a device implanted in Angie's skull: her father had apparently altered her nervous system to allow her to access the Cyberspace Matrix directly, without a "deck" (a computer with an interface directly into the user's brain), but she is not conscious of this. During their stay, Turner has a one-night stand with Sally, and then leaves for the Sprawl with Angie where he meets with Bobby's group in a shopping mall besieged by agents of Maas and Conroy.
Thread Two : In Barrytown, New Jersey a young amateur computer hacker, Bobby Newmark, self-named "Count Zero", is given a piece of black market software by some criminal associates "to test". When he plugs himself into the matrix and runs the program, it almost kills him. The only thing that saves his life is a sudden image of a girl made of light who interferes and unhooks him from the software just before he flatlines. After fleeing his house (which is immediately thereafter destroyed) he meets Lucas, Beauvoir and Jackie, a group fascinated by and dedicated to the recent appearance of voodoo deities in Cyberspace, who take him into their protection as they are collectively targeted by various corporate agents. It is eventually revealed that Bobby's mysterious savior is Angie (see Thread One); the two only meet physically at the very end of the book.
Thread Three : Marly Krushkova, a small gallery owner in Paris until she was tricked into trying to sell a forgery, and newly infamous as a result, is recruited by ultra-rich, reclusive (e.g. Howard Hughes) industrialist and art patron Josef Virek to find the unknown creator of a series of futuristic Joseph Cornell style boxes. Unbeknownst to her, the reason behind Virek's interest in these boxes is related to indications of biosoft construction in the design of one, which he suspects may be contained in the others.
All of these plot lines come together at the end of the story and Virek– the hunter of his immortality and unlimited power – becomes the hunted. It is hinted that multiple AIs secretly inhabiting cyberspace are the fragmented, compartmentalized remains of two AIs, Neuromancer and Wintermute, having joined together (introduced in Neuromancer , and designed by the head of this Rockefeller-like family, the Tessier-Ashpools). These AI units now interface with humanity in the form of different Haitian voodoo gods, as they have found these images to be the best representations of themselves through which they can communicate with people. Hackers worldwide are becoming aware that there is something weird loose in the cyberspace matrix, but most are understandably reluctant to talk about (or deal with) "voodoo spooks" supposedly haunting cyberspace. The "voodoo gods" have constructed the elaborate series of events in the novel, having originally given Mitchell the information for developing the biosoft, instructing him to insert a biosoft modification in his daughter's brain, and then sent the Cornell boxes into the world to attract, and enable the disposal of, the malicious Virek. A pair of epilogue chapters resolve the fates of the protagonists, at least until Mona Lisa Overdrive . Angie has attained celebrity status as a simstim star, and has entered a relationship with Bobby who is employed as her 'bodyguard'. Marly has returned to Paris and now curates one of the largest art galleries in the city. Turner has returned to his childhood home (the same one occupied by Rudy and Sally earlier in the book) to raise the child conceived during his affair with Sally; Rudy was killed by Conroy's agents when they were trailing Turner and Angie.
The Cyberspace Matrix, a synergistic linked computer database that encompasses all information on Earth, has become home to sentient beings. But most of humanity remains unaware.