Legend is set in a flooded, fortified, and futuristic version of Los Angeles, ruled by the totalitarian Republic of America. The novel centers around Day (Daniel Altan Wing) and June Iparis, two 15-year-olds on opposite sides of the economic spectrum. June Iparis is a military prodigy, born into an elite family, and groomed for success in the Republic's highest circles. She is the only person to have ever scored full marks on the Trial, a comprehensive test administered at age 10 to determine the child's future role in society. Her parents died several years before the start of the story, so she is raised by her older brother Metias. Daniel "Day" Wing is an infamous wanted criminal, born in the impoverished slums of the Republic. His family believes he is dead, apart from his older brother John.
Day learns that his younger brother, Eden, is infected with the Plague, a disease that periodically ravages sectors of the Republic. Day breaks into the city hospital to steal medicine and escapes after a confrontation with Metias. Later that night, June is informed by Thomas, an officer in the Republic and Metias's childhood friend, that her brother was murdered by Day. June graduates early from her military university and sets out to catch Day. Using the promise of a cure for Eden's infection, she lures Day to the site of one of his previous heist locations, and they converse, albeit not face-to-face, before Day realizes she is a Republic agent.
June poses as another person from the sector searching for Day. She gets in a street fight, stepping in for Tess, and beats the previous champion, Kaede. June is stabbed in the process. Day rescues June, unaware of her identity, and Tess, a friend of Day's, sets about healing June. Day and June begin to develop romantic feelings for each other, eventually culminating in a kiss, but June realizes who he is and reports his family's location to Thomas and the Republic. Day attempts to defend his family's house from Republic soldiers, but Thomas kills his mother and Day is captured.
As June questions Day, he insists he is innocent of Metias's murder. June reviews Day's files and discovers he got a perfect score on the Trial, like June herself. However, instead of Day being celebrated as a prodigy, the Republic falsified records to indicate Day failed his Trial and died in a labor camp. While Day is being moved to a new cell, he sees evidence that the Republic is intentionally spreading the Plague. Day is further tortured by Commander Jameson and sentenced to death.
June informs Day that John is in a cell and Eden has been sent to labs on the war front. Day tells June about painful tests inflicted on him after supposedly failing the Trial. Children sent to "work camps" are actually killed or used for experimentation in laboratories; Day escaped after being left for dead. Day tells June his theory about the origins of the Plague. Later, protestors gather in support of Day; June watches Thomas order his soldiers to fire on the protestors.
That night, June determines that Metias was actually murdered by Thomas, under the orders of Commander Jameson. Metias left a coded message for June, revealing that their parents were murdered for discovering the true purposes of the Plague: a method of culling the weaker Republic populations, and a biological weapon against the Colonies. June decides to break Day and John out.
June and the Patriots plot an escape plan, but Jameson moves up the execution date. June attempts to rescue Day and John on her own but is arrested by Thomas. Their confrontation is halted by attacking Patriots, and June escapes with Day in the chaos; John sacrifices himself to allow June and Day to escape, and the Republic, having mistaken John for Day, claims that Day has been executed. Day and June decide to head to the war front labs to rescue Eden and then escape into the Colonies.
