Gold-Eye, a fifteen-year-old, was born near the time of the Change. He was physically affected by the Change radiation and his eyes, including his pupils, are a bright golden color. He has a very special talent known as being able to see in the "soon to be now." He is also unusual in that he managed to escape and elude the Trackers and Myrmidons for a time. Yet as the story begins, he is finally trapped by the Myrmidons, and prepares to kill himself to prevent his organs from being harvested. This turns out to be unnecessary as he is saved by a team of strangers who stun the Myrmidons with a flashbang grenade and lift him to safety. These strangers are a team of Shade's Children, and after the group eludes some Ferrets by hiding in a tall building, he accompanies them back to the Submarine, Shade's Children's hideout.
Gold-Eye joins Shade's Children, and is soon sent off on his first mission with the team that saved him: Ella, Ninde, and Drum. Each team member is unique, and has Change abilities that correspond somewhat to their personality.
This mission is a critical one: to retrieve the equipment and data from Shade's abandoned laboratory on the University campus in the Department of Abstract Computing, including a device that measures Change radiation. It is also one of the most dangerous missions: All of the teams who have previously attempted this retrieval have been killed or captured in the process. Ella's team is successful, even when the Overlord Black Banner surrounds and invades the building, alerted by Leamington, a pre-Change artificial intelligence who calls the police on detection of the intruders. Leamington is notably different from Shade in that he is an artificial intelligence as opposed to an uploaded consciousness.
After resting at the Sub, Shade unveils the reward created with the recovered data: metal crowns called Deceptors which scramble the sensory input of the Overlords' creatures, effectively making a human wearer invisible and non-olfactive to them as long as the power supply is maintained. It also is later revealed that scent trails are equally scrambled, although footprints are not. With this sudden new advantage and information, Shade is more curious about the method of distribution of Change radiation and sends Ella's team on a newer, even more dangerous mission: to steal a Change Projector from Fort Robertson, the stronghold of the Overlord named Red Diamond. This mission is not successful: on entry, the team discovers that the stronghold stretches underground, allowing for the unforeseen presence of creatures. The team's Deceptors run out prematurely as they discover a Myrmidon barracks, and they escape with a conch-shaped Overlord device called a Thinker, but without Drum who, having been winded, stays behind to fight. It is presumed by the rest of the team that he is killed.
On return to the Sub, however, Gold-Eye has a vision in which he sees Drum being stored temporarily in the Meat Factory, indicating that Drum is still alive. The group presents the device to Shade, who appreciates the Overlord device Ninde took from Fort Robertson but refuses a request to rescue Drum, as the Meat Factory is one of the most heavily guarded Overlord facilities.
The team, led by Ella, defies Shade's orders and infiltrates the Meat Factory, successfully rescuing Drum. They then leave cautiously, using the Deceptors to mask their trail. While resting among the branches of a large tree, Ninde telepathically detects an Overlord. The detection proves not only to be hard mentally on her since the Overlord is of human or greater intelligence, but also emotionally hard: Ninde discovers that the Overlords are essentially human. Despite the difficulty, she discovers that the Overlord may know something about "a mind in a machine" -a dangerous thing for them, since Shade - a machine intelligence- is their leader and benefactor. They continue, to discover on reaching the Submarine that it has been invaded by an Overlord, Red Diamond, and that all of the people inside have been killed or captured. Fortunately, Shade had realized long before that the Sub was not a permanent base, and established multiple supply caches throughout the city in case a team was stranded in the field or the Sub was taken. True to their training, the team heads immediately to the nearest cache - to discover Shade, who escaped, apparently by chance, while testing a mobile robotic body for himself based around the Thinker. Shade's escape is doubly fortuitous in that the Overlord used an electromagnetic pulse weapon to disable the Submarine; had he been within range of the weapon, he would have been incapacitated.
Despite the loss of all of Shade's Children except for Ella's team, the meeting is a good one: Shade has discovered how to defeat the Overlords. Examining and measuring Change radiation, he had discovered that all known Change Projectors were actually redistributors of Change radiation from a single source, a so-called Grand Projector. Were this projector destroyed, all creatures would cease to function, and the Overlords would likely be removed whence they came. Having discovered the source of the Change Radiation - at Mount Silverstone - they set out with Deceptors to find and destroy the source, which would hopefully bring reality back to normal.
But soon the team is betrayed by Shade, who had made a deal with the Overlords. Desiring a body with which to survive the Overlords' destruction (since the Thinker is also a product of the Change), he betrayed the children, bartering them and the knowledge of their Change talents in exchange for Overlord body technology (his Thinker is destroyed by an Overlord later). Gold-Eye and Ninde are taken prisoner. Ella and Drum, managing to escape, climb to the top of Mount Silverstone, meet a hologram of Shade, who though having been physically destroyed, is spread through the Overlords' computer systems. His original personality had been attempting to manifest itself, such as when Shade was speaking to Gold-Eye and Ninde about their fate at the hands of the Overlords, or when Shade was inwardly arguing with himself. However, it only managed to when the Thinker was destroyed. He guides them to the Grand Projector, when, about to disable it, they hear an Overlord approaching.
Ella, desperate, destroys the Thinker which regulates the Grand Projector, causing it to overload. This has the positive effect of disabling all Overlord creatures and removing the Overlords, but exposes Ella and Drum to lethal amounts of Change radiation, killing them. The burst of Change radiation, while not lethal where Ninde and Gold-Eye are (they are being executed by an Overlord), enables them to respectively read the minds of thousands of newly freed children, and see a distant future, at which time he and Ninde are the parents of two children named for Ella and Drum. Ninde sends this "soon to be now" to Ella and Drum through her Change Talent, and those thoughts are the last things that they see.