The story centers around two teens and tithe who have been scheduled to be unwound. They are all runaways, which is known as "kicking AWOL"; Connor, a sixteen-year-old whose family believes he'd gotten into too many fights, Risa, a ward of the state who doesn't make it in the State Home's continuing program because of budget cuts, and Lev, a tithe whose rich parents had him specifically to be unwound, as he is the tenth child. Lev and his family believe 10% of everything they have should be given to the Church, including Lev.
Connor discovers his unwind order and decides to "kick AWOL", and tries to convince his friend Ariana to go with him. She agrees but later backs out, and he runs off alone with the help of a trucker. However, his cell phone tracker gets him caught. Connor resists arrest and flees the Juvey-cops, running into traffic and snatching a tithe (Lev) from a car to use as a hostage and human shield. The chaos which ensues causes a bus full of State Home wards (StaHo kids) on their way to the harvest camp to overturn, and provides Risa with the perfect opportunity to escape. Risa, Connor, and Lev flee into the woods, and are pursued briefly by a Juvey-cop, whom Connor shoots with the officer's own tranquilizer gun after he is baited by Risa.
The next morning after their usual sacrificing of a baby goat, while gathering supplies, the three come across a storked baby on a doorstep nearby. Because of a past experience, Connor can't just pass by, and puts them all at risk by picking up the baby in plain view of a cop car cruising nearby. The three get on a school bus to blend in and hide out in the school bathroom with the baby. Lev takes his chance to escape, because as a tithe, he believes that it is an honor to be unwound, and he goes to the school office to turn in the others. He calls his pastor after he's done so, who tells him he helped keep their faces out of the paper so Lev could be free. Astonished by this sudden change, Lev pulls the fire alarm to help Connor and Risa escape from the incoming cops.
Connor and Risa attempt to hide, but are discovered by a teacher, Hannah, who helps them to escape the school and tells them to go to an antique store and ask for Sonia, who will help them. The store is a safe house, where they stay for a few days before the Ice Cream man comes to pick them up and shuttle them to another house in the chain. Before they leave, Sonia has them and the other kids, named Roland, Mai, and Hayden, write letters to their loved ones about how they felt about being ordered to be unwound and said she would mail them if they didn't come to collect it a year after their eighteenth birthdays, when they would be safe from unwinding. Hannah comes to say goodbye, and to take the baby, whom she and her husband have decided to adopt and claim as a storked baby. The escaped children are eventually taken to a holding area, a big warehouse by an airport.
Lev, in the meantime, has also managed to escape and has met up with a kid named Cy-Fi who claims not to be a runaway, but is headed to Joplin, Missouri because 1/8 of his brain, the right temporal lobe which he got from an unwound youth instead of bits and parts like it's usually done, would take over his mind at times and he needed peace. Cy-Fi teaches Lev some street smarts along the way, and Lev helps him and the unwound kid inside him get closure.
At the warehouse, Risa begins to understand the power games Roland is playing in breaking up any groups of kids that might be a threat to him. She tries to make Connor understand and stay calm, as a fight between the two of them is looming as Connor appears to be the next biggest threat to Roland. Connor takes her words to heart and isn't baited by Roland when he attempts to rape Risa in the bathroom. Shortly after, they are all taken to the Graveyard, an aircraft graveyard, their final destination and where they will remain until they reach the age of eighteen and are safe.
A former admiral is in charge of the airplane graveyard and assigns the children to work detail where they can best be used. Connor becomes a mechanic and Risa becomes a medic, while Roland learns to fly a helicopter from Cleaver, the only other adult who knows about the kids. Roland starts up his trouble anew, spreading stories about the Admiral to sow dissent and to make himself the new leader. Connor ends up on the Admiral's side as a spy, and when a number of the higher up kids are killed, they investigate, believing Roland to be responsible. A short time in, Lev arrives, tougher than before, and joins a secret group that wants to damage Unwind facilities rather than just live out to age eighteen and then leave the camp.
The Admiral has a heart attack during a riot caused by doubts sown by Roland, even though he is not there to direct it and take over. Connor brings things under control, and gets Roland and Risa to come with him to fly the Admiral to a hospital, knowing they will likely be caught. They are taken away to a harvest camp, where Risa unwillingly joins the band which plays at the unwinding and death of each child.
Lev is at the camp as well, having turned himself in after becoming a clapper, a suicide bomber who has been injected with a liquid explosive triggered by clapping hard enough. Roland is unwound due to his blood type being high on demand. Just as Connor is about to be unwound, the other two clappers, Blaine and Mai, who are at the camp with Lev detonate their explosives at his request. He intends to join them, but at the last minute changes his mind, determined to pull out unwound youth from the wreckage and save Connor. He does so, and turns himself to the police.
Back at the hospital, Connor and Risa unite again. Connor's injuries made them the unwilling recipient of a new eye, and an arm that formerly belonged to Roland, which they can tell from the shark tattoo on the arm. The nurse gives him a fake ID from a guard killed in the explosion to save him from unwinding. Risa refuses treatment despite being paralyzed from the waist down, and saves herself that way as well, as disabled people cannot be unwound. Lev is saved by the explosive fluid in him, which is slowly being removed from his bloodstream.
Risa and Connor return to the Graveyard to run it because the Admiral is too weak, having refused to take a new heart from an Unwind. They promise to begin fighting against harvesting. The story ends with a party at the Admiral's house, celebrating the birthday of his son, whom he and his wife unwittingly had unwound. All the people who received parts from his son attend, bringing him entirely there.
At the end of the book, Connor becomes the new Admiral for the Graveyard. This book has a sequel which is titled Unwholly.