In a dystopian USA, a contagious disease called Idiopathic Adolescent Acute Neurodegeneration kills nearly 98% of all children and teenagers, leaving the survivors with unusual abilities. These survivors with superpowers are imprisoned. Ruby Daly is an orange which means she has the psionic ability to get into people’s mind. She escapes her prison and joins a resistance group (League) to fight for her future. Cate, a worker at the camp, provides Ruby with a panic button that can be activated as a tracker if she is in danger. When Ruby gets visions while touching Rob, another League member, she becomes suspicious of their intentions. Ruby makes her escape with a mute little girl named Suzume (Zu), a Yellow. Zu takes Ruby to Liam, a Blue, and his friend Charles (Chubs), a green. The three agree to let Ruby join them as they try to make their way to “East River,” a purported safe haven led by an Orange named Slip Kid.
The four enter an abandoned mall to gather supplies, where they cross paths with another group of survivors. The others know where East River is, but the only clue they reveal – due to the subtle influence of Ruby’s power – are the letters “E D O”. Chubs eventually deduces that this is a radio frequency, which reveals a transmission that East River is in Lake Prince, Virginia.
Journeying to East River, Ruby and Liam begin to develop a romantic connection, but Ruby refuses to touch him, fearing that her powers will hurt him. At East River, Slip Kid is revealed to be the president’s son, Clancy Gray, who is an Orange. He teaches Ruby how to control her powers, and in return, has Ruby teach him how to erase people’s memories. During this process, Clancy controls her mind and kisses her.
It is revealed that Clancy is using his powers to control the government, and wants to use his new memory-erasing powers to turn Ruby to his side and forget her friends, but she manages to escape with the others. Liam flees with all of the haven kids, while Ruby faces off against Clancy, destroying the camp and making her escape with Chubs. Chubs is severely injured, leaving Ruby no choice but to use her panic button to call the League for help.
The League gets Chubs to a hospital and lets Zu leave with a protective family. Ruby convinces Cate to release Liam in return for taking his place as a soldier in the League. Knowing that Liam will never leave without her, Ruby kisses him and erases all of his memories of her. Liam leaves the camp, while Ruby begins her training with her fellow powered kids in the League. Elsewhere, Clancy looks over his army of government forces.