The world looks different in Logan Langly’s time. Natural disasters have led to unrest. Epidemics and battles ensued in Europe and the United States, leading to what became known as the Total War. American leader Lamson and European Chancellor Cylis rose up to implement a period of Unity. They lumped all world religions into a patriotic belief system called Inclusion to ensure a Total War would never happen again. Now, the government monitors citizens by Marking them at age 13. The Mark allows them to get jobs and buy food and entitles them to other societal privileges. Those who protest and remain without the Mark, the Markless, become outcasts and are relegated to lives of poverty. A government agency called DOME (Department of Marked Emergencies) handles the Marking process, as well as keeping an eye on the Markless.
Logan, nearing his 13th birthday, is concerned. He remembers too well how the government mysteriously pronounced his sister, Lily, dead on her Marking day. Besides that, he feels that he’s being watched. Elsewhere in Logan’s town of Spokie, 13-year-old Erin Arbitor unpacks some of her father’s mysterious boxes. Mr. Arbitor has moved them to Spokie, leaving her mother in their hometown of Beacon, so he can pursue a top-secret government project for DOME.
Determined to put her family back together, Erin looks for clues to help her father solve his case. She learns he is pursuing a Markless boy named Peck, who appears to be kidnapping children just before their 13th birthdays. When she meets Logan at school, he tells her about his sense of being watched. She becomes convinced he is one of Peck’s next targets.
Peck’s underlings, Markless young people known as The Dust, lure Logan to a park at night. They abort a plan to abduct him when they learn he has an accomplice and that Erin has procured stealth surveillance equipment from her father’s DOME office. The previously fearful Logan begins to aggressively pursue his would-be kidnappers with Erin’s help.
Peck finally captures Logan, but Logan learns Peck isn’t the enemy. Peck explains the truth about the government’s Marking system. He tells Logan that DOME disposes of people, such as Lily, who may be handicapped, slow, or seem predisposed to undermine the government’s ways. Logan decides to get his Mark on his birthday as an undercover operation. He already suspects DOME will reject him as they did his sister.
During the process, he learns from a remorseful Marker that Lily is alive in Beacon. Erin helps Logan escape from the Markers, but she says she will do no more to aid him in his new cause. They sadly part ways, and Logan makes plans to go to Beacon to find Lily.