Sixteen-year-old Ruby has been in Thurmond Rehabilitation Camp for six years. The government-run institution was supposedly created to help the children mutated by a bizarre plague return to normal life. The plague, which strikes children after the age of 10, either kills them or leaves them with supernatural abilities. Those mutated are divided into categories. Blues and Greens can throw things with their minds or control natural elements. Yellows cause electrical things to malfunction or burst into flames. The most dangerous categories are Oranges. These children can manipulate people’s minds, and Reds are those who can create fire.
Ruby was placed in the camp on her 10th birthday when she accidently erased her parents’ memories of her. Through a series of government mistakes, and Ruby’s newfound ability, she was able to get herself designated as a Green, thereby escaping the worst of Thurmond’s rehabilitation techniques. When the public’s fear of the Oranges, Yellows and Reds becomes too great, those children are taken away, never to be seen again.
The officials of the camp use a special white-noise broadcast to incapacitate the Psis, as the children are called, when they act out against authorities. A new version of the noise renders Ruby unconscious. When she wakes up in the infirmary, she meets Dr. Begbie, a beautiful woman who treats Ruby with kindness. Before she leaves, Dr. Begbie slips Ruby a note saying that the authorities know now she’s an Orange and plan on killing her. She will help Ruby escape that night, if Ruby is willing to take the risk.
Without much of an option, Ruby takes the pills Dr. Begbie gives her, which induce a seizure. Dr. Begbie disguises Ruby in another doctor’s scrubs and slips her out of the infirmary and into her car. Later, Ruby learns her savior is not a doctor but Cate, a member of the Children’s League, an anti-government group that wants to destroy the rehabilitation system. Ruby realizes that Cate has rescued her and another boy in order to make them soldiers in the League’s guerilla war. Ruby hates that she can erase people’s memories and does not want to be used in anyone’s schemes. She escapes from Cate and winds up with another group of Psis living on the run and in a van.
Eventually, Ruby comes to trust her three new friends. Chubs and Liam are boys a little older than her who are Blues. Zu is a younger Asian girl who no longer speaks and is a Yellow, causing mechanical things to explode when she touches them. Ruby tells the others that she is a Green as she is afraid of their reactions if they learn the truth. She makes every effort not to touch them so she will not accidently erase their memories. The others are on the run from skip tracers, bounty hunters looking for Psis. Liam and his friends are especially wanted because he organized the only successful escape from a rehabilitation camp. It was successful because at least some Psis escaped, but Liam lives with the grief that hundreds more were killed in the attempt. Liam and Ruby begin to fall in love.
Liam and the others are trying to locate an almost mythical figure known as Slip Kid. This boy supposedly runs a camp for refugee Psis called East River, and can help them locate their parents. Every new lead they hear about the Slip Kid turns up a dead end until Ruby finally puts several clues together and realizes that they need to tune in to a certain radio frequency. Through the random noises comes a message only Psis can hear, telling them where there is a safe place for them to hide. Before they can reach the camp, the skip tracer who has been tracking Liam and the others since their escape finds them. Ruby reluctantly uses her abilities to wipe the woman’s memory of their encounter. She then implants the order of the woman’s walk into the woods and has her believe that she is not to leave the woods, or eat, or drink, or move, ever again. Ruby is afraid her new friends will abandon her now that they know her true powers. They admit they figured it out long ago and still accept her.
Ruby and the others accidently find the camp of the Slip Kid when they come upon a guerilla raid on an overturned tractor trailer. They are taken to East River and welcomed as part of the refugee camp. Liam, Chubs and Zu are given new jobs that they must do in order to stay, but Ruby becomes the special project of the Slip Kid. He is really Clancy Gray, the president’s son and poster boy for Psi rehabilitation. Clancy’s portrait is displayed all over the camp as proof that rehabilitation can work, only Ruby learns it’s a lie. Clancy is an Orange and can manipulate people’s minds. He used his power to convince his father and the doctors that he had been healed. Although Clancy claims to be trying to help Ruby develop her abilities, all she experiences are disconcerting episodes where Clancy delves into her memories. Clancy also tells her that Cate and the Children’s League were the people who sabotaged Thurmond’s white noise system so they could find hidden Oranges and Reds and turn them to their cause.
Clancy and Ruby spend many hours a day together. Although Ruby occasionally feels as though her thoughts are not her own, she continues to trust Clancy and tries to learn from him. As Ruby finally gains control of her abilities, Clancy has her try them out on other campers. She convinces one girl that her name is Theodore. The girl cries whenever the other campers call her by her real name.
Ruby observes Clancy’s ability to calm the other kids when he touches them. She thinks he has natural leadership qualities, not that he is using his psychic capabilities to manipulate them. But then one day he sexually assaults her. He uses his powers to keep her from fighting against him and clouds her memory of the incident, so she cannot be sure it actually happened. When Ruby regains full consciousness, she flees from Clancy’s room.
Liam finds Ruby hiding and afraid. When they embrace, Ruby somehow manages to slip the memory of Clancy’s assault into Liam’s mind. Furious, he insists that they get Chubs and leave the camp that night. Before they can escape, Clancy arrives with his security team. He freezes Liam’s muscles with his mind, then has a member of his team beat the defenseless boy to a pulp. The three are returned to their cabin.
A hysterical girl arrives some time later begging Ruby for help. Clancy has collapsed with a seizure and is bleeding. Ruby follows her to find Clancy, but only to hopefully use her powers against him now that he is weak. Instead of in the throws of a fit, Ruby finds Clancy upright and rational, but pushing an image of himself into the other girl’s mind.
Ruby tries to convince Clancy into letting her and her friends go, but Clancy is too strong. As sirens break through the night, the camp is overrun with soldiers killing the children. Clancy believes it is an army of Red Psis that he has specially trained. Instead he discovers it is government soldiers. His father, the president, must have discovered Clancy’s plan and is now set on exterminating every child in the camp. Chubs rescues Ruby from Clancy and the soldiers.
Once the soldiers evacuate the camp, Ruby and Chubs return to use Clancy’s laptop to locate a friend’s family. Chubs has promised to deliver a letter to them. Liam finds them there and the three set off together. Sadly, when Chubs tries to deliver the note to his friend’s father, the man shoots him.
Desperate to save her friend, Ruby presses an emergency button given to her by Cate. The Children’s League arrives a few minutes later. Liam promises to do anything the League wants as long as they take the dying Chubs to a hospital. Ruby is drugged and falls unconscious.
When she wakes up, Cate tells Ruby that she is in a safe house. Chubs arrived at a hospital, but Cate has no idea if he is still alive. Ruby agrees to stay and fight with the League if they will let Liam go. Knowing that he will never willingly leave her, Ruby erases his memories of her. As Liam walks away from the safe house, Ruby thinks about how much she has changed in the past few weeks. She will reluctantly fight with the Children’s League, but she will try and keep some untainted part of her secure in her mind.