Day, the Republic's fifteen-year-old most wanted criminal, breaks into Los Angeles Central Hospital in hopes of stealing a cure for the plague that threatens his family. While escaping the hospital, Day loses the pendant his father gave him and allegedly kills Metias Iparis.
June, a fifteen-year-old prodigy, is chosen to find and capture Day, who is charged with the murder of Metias Iparis (June's older brother), among other crimes against the country. Though she was born into an elite family in one of the wealthiest districts in the Republic, June poses as a girl from the slums in order to search for Day, coincidentally collecting Day's fallen pendant as she observes the crime scene. When attempting to lure Day by pretending to be a merchant with a plague cure that doesn't work, June decided to look for Day herself.
After getting injured in a 'Skiz' fight, June is circumstantially taken into the care of Day and his young partner in crime and only friend, Tess. Day then kisses June in an alley while being in a half-drunk condition due to the wine he was drinking. But still, he felt affection for June. June turns him over to the Republic once she figures out that her saviour was indeed Day, the criminal that her commissioner sent her to arrest.
The next morning, military medical trucks and soldiers surround Day's home. As Day rushes to save his family, June follows him, but the military captures Day's family, forcing Day out of hiding. He tries to resist capture, but Thomas, Metias' and June's close friend, shoots Day's mother under order, killing her. Day reacts by trying to kill the soldiers in vain. Commander Jameson, June's commanding officer, shoots Day in the leg.
Day wakes as a captive of the Republic. After June returns from her mission, Thomas starts pursuing her romantically. Day is questioned by June, Commander Jameson, and eventually Thomas, who has a personal hatred for Day because he kissed June.
The more Day speaks with June, the closer they grow and the more they come to understand each other. She finally researches Day's real identity - Daniel Altan Wing - and discovers he scored a perfect score on his Trial, just as she did. The authorities have told Day that he had failed his Trial, which is what Day has come to believe. While June was moved into a prestigious program because of her high Trial score, Day was experimented on and abandoned, supposedly dead like the others who failed their Trial.
Day confesses that he did not kill Metias but had only injured him.
June seeks out Kaede, who is the one who injured June in the Skiz fight and one of the Patriots, a group of anti-Republic rebels. She finds that Tess has taken refuge with them after Day is taken by the Republic. June negotiates with the Patriots for their help, freeing Day on the morning of his execution. The plan does not perfectly execute, as Commander Jameson moved up the execution time, and Day's older brother John sacrifices himself by posing at the execution as Day so June and Day can escape.
Three days later, June and Day take shelter in an old train car and plan to go to Las Vegas, where the Patriots are, so they can check on Tess before heading out to find Day's little brother Eden. Day also explains why he chose his nickname, saying that everything happens each day, and that everything can be possible the next day. "'You try to walk in the light.'"