Jack Forman, who is an unemployed software programmer who used to work with artificial intelligence. He is fired for attempting to expose an internal scandal in his company, MediaTronics. As a result, he is forced to take the role of "house-husband" while his wife Julia works as vice-president for Xymos, a nanorobotics company. Julia claims that Xymos is on the verge of perfecting a revolutionary new medical imaging technology based on nanotechnology.
The story starts with a series of strange events happening in rapid succession. Jack's baby daughter Amanda develops a very strange painful rash that propagates and becomes very severe. While the doctors are unable to find the cause of the rash, an MRI scan instantly cures her. Amanda's room is visited by a special team of Xymos personnel. Later, Jack is surprised to see the memory chip of an MP3 Player belonging to his son corroded into powder. During this time, Jack also begins to suspect that his wife, who comes home very late and shows aberrant behavior, is having an affair. MediaTronics contact Jack, explain to him that they have become a contractor of Xymos and offer to rehire him to help deal with an alleged software problem for Xymos. The following night, Julia hastily leaves home shortly after arrival to go back to work. Jack and his son both see what looks like the silhouette of a man in her car, although Julia denies it. Julia's car crashes in the road. At the scene of the crash, Jack spots the Xymos special team in a van, wearing strange gear.
Convinced that Xymos is somehow connected to all these strange events, Jack accepts MediaTronics' offer and travels to the Xymos manufacturing facility, known as "fab plant", in Nevada. At the fab plant, he is joined by members of his old software development team - Mae, Charley, David, Rosie, Bobby and Ricky. Ricky, now working for Xymos and in charge of the fab plant, gives Jack a brief tour of the building, and explains that the company was under contract from the Department of Defense to create a swarm of nanorobots that act as a camera for reconnaissance and spying. The swarm is created by genetically modified E. coli bacteria, which create gamma assemblers from raw materials that, in turn, manufacture nanobots.
Ricky reveals that building contractors failed to properly install filters in a certain vent in the building. As a result, hazardous elements such as the assemblers, the bacteria, and the nanobots were blown into the desert, evolving and eventually forming autonomous swarms. These swarms appear to be solar-powered and self-sufficient, reproducing and evolving rapidly. The swarms exhibit predatory behavior, attacking and killing animals in wild, using code that Jack himself worked on. Most alarmingly, the swarms seem to possess rudimentary intelligence, the ability to quickly learn and to innovate. The swarms tend to wander around the fab plant during the day but quickly leave when strong winds blow or night falls.
The nanoswarm kills a rabbit outside the complex, and Jack goes outside with Mae to inspect. They find that the rabbit died of suffocation resulting from the nanobots blocking its bronchial tubes. While Mae goes inside for equipment, Jack is attacked by the swarms. He barely manages to get through the airlock inside the lab before falling unconscious from anaphylactic shock.
The team explains to Jack that they believe Julia is the reason the swarms wander around the plant: During the earlier days of swarm appearance, Julia had started an attempt to make personal contact with them, first "entertaining" them with kid toys and then testing their intelligence using colored blocks. As time passed, Julia gained more affection for the swarms. In turn, the swarms, especially one of them, developed an affinity toward her.
Persuaded by Jack, the team decides to destroy the swarm. They believe that the swarm must have nested in the desert to reproduce. They attempt to find this nest by tagging the swarm with radioactive isotopes and following them back to their nest at night. Under the cover of a strong wind that forces the swarms to remain dormant, the team goes outside to a storage shack to find the isotopes and build a spray device. However, as the wind dies down, four swarms attack the shack and eventually kill David and Rosie. The rest of the team are forced to take shelter in the cars parked outside. The Swarms begin an attempt to enter the cars.
The team notices that these swarms are more advanced than the ones they saw before. They are capable of tracing tracks, tripping their prey by making the ground slippery, taking snapshots of their prey and forming a flat surface to display rudimentary still images.
Eventually, the swarms find a way to enter the cars, but not long before the wind picks up in speed again. Jack and Mae manage to escape to the lab before losing consciousness, but Charley falls unconscious outside his car after he sprays his swarm with the isotope. Bobby, Vince and Ricky refuse to go outside and help Charley. Jack, dizzy and nauseous, goes back out again to save Charley as the swarms attacks again. Using a motorbike found in David's car, Jack manages to get himself and the semi-conscious Charley to the safety of the airlock before he falls unconscious again.
During the evening, security cameras show another alarmingly more evolved swarm in the vicinity of the facility that can form into a 3D replica of Ricky. This swarm acts as a decoy while other swarms stealthily carry away the dead corpses of David and Rosie.
As night falls, Jack, Mae and Bobby set out to find the swarms. While searching for them, they discover that one of the swarms, now so evolved that it can operate without solar energy, is moving the now deceased Rosie through the desert. They follow the body to find the swarms nesting in a cave. As some of the swarms come out of the cave after them, a Xymos helicopter arrives and traps the swarms inside the cave using its powerful draft. Mae and Jack then venture into the cave and proceed to exterminate the swarm, their nest and their organic assembly plant (which looks very similar to the original Xymos assembly plant) using explosive thermite caps. They return to the Xymos plant, exhausted.
At the plant, Jack, Mae and Bobby are enthusiastically greeted by Julia, who was earlier discharged from the hospital and was brought in by the chopper. Julia's behavior seems to be extremely aberrant: She seems to heed to nothing else other than trying to entice Jack and kissing him, even when Charley is found dead in the locked communications room with a swarm flying around him and the communication links cut. Jack cannot understand how the swarm got inside the rigorously protected airtight building, why Charley would have disabled the facility's communications, or why Julia and Ricky seem to be coming up with various out-of-character ways of how he died.
Jack wakes up early the next day and finds Mae looking over a security camera's video. To Jack's horror, the video not only reveals that Julia and Ricky had an affair but also shows how Charley engaged in a vicious fight with Ricky and Vince. All of them end up in the communications room where Julia kisses a subdued Charley, injecting a stream of swarm into his mouth.
Eventually, Jack and Mae realize that everyone in the facility except themselves have been infected by a symbiotic version of the nanobot swarms. These nanobots, although evolved alongside the other swarms, do not show aggressive predatory behavior. Instead, while they seem to invigorate their hosts' physical statistics and their perception, they slowly devour and take over their hosts, initially affecting their decisions and then controlling them, while allowing them to travel and contaminate others.
Jack comes up with a plan to destroy this new strain. Mae and Jack drink vials containing a form of phage that kills the nanobot-producing E. coli bacteria. The phage would protect them from infection. Jack then proceeds to take a sample of the phage and pour it into the sprinkler system and drench everyone with it. He tricks Mae into alerting Julia and the infected team. They set out to stop Jack. In the vicious struggle that ensues, Vince is killed and Jack, who barely escapes death multiple times, finally manages to dump the sample into the sprinkler system.
In order to prevent the sprinkler system from triggering, infected-Ricky disables the plant's safety network. However, this is exactly what Jack wants, as Mae has already allowed the phage into the assembly line, causing the phage to reproduce rapidly. The assembly line is rapidly overheating because of the no longer active safety system. If Ricky and Julia do not turn on the safety system the assembly line will burst, filling the lab with the phage. The infected-team, who are now doomed either way, choose to re-activate the safety network and get drenched with the phage. Jack and Mae escape the facility in a helicopter shortly before the facility explodes due to a methane gas leak combined with thermite Mae has placed in the building. After returning home, Jack infects all his children with the phage to eradicate the potential nanobot infestation. Mae calls the U.S. Army and sends a sample of the phage to her lab.
Jack puts together all the missing links. The corrosion of the memory chip in Eric's MP3 player as well as Amanda's rash were caused by gamma assemblers. The MRI's strong magnetic field detached the assemblers from her. These assemblers were most likely brought home by Julia. Knowing this, Julia called in the Xymos special team to scan Amanda's room. The person who Jack spotted in Julia's car was in fact the cloud of nanobots.
Jack also discovers an e-mail on Julia's laptop that indicates that the release of the swarm in the wild was not accidental. Julia had authorized the release of the swarms in the first place in hopes that it would evolve and solve their problem, failing to realize the potential consequences of their actions. Consequently, one of the swarms infects Julia and then Ricky.
The story ends with Mae returning to Jack's house, with a bottle of the swarm.
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