After the "Heartland War," a civil battle between those who believed in abortion on demand and those considered to be pro-life, a set of constitutional amendments was passed called "The Bill of Life." These amendments stated that from the moment of conception, human life couldn't be ended. But, from the age of 13 until a child reaches 18, a parent or guardian may choose to retroactively abort their child. This process is called "unwinding." The child is not technically killed, as every useful piece of its body is recycled into the bodies of other people in need.
Connor Lassiter, a 16-year-old troublemaker, has discovered the papers his parents have signed ordering his unwinding. He escapes before the authorities come for him, but the Juvenile Police, or Juvey-cops as they are known, and his parents track him through his cellphone. Connor doesn't give up easily, and instead flees across a divided highway as the police shoot tranquilizer darts at him. A Cadillac sideswipes him. Inside is Lev Caldor, a 13-year-old boy, willingly being unwound as a tithe to God. Connor makes the snap decision to use Lev as a shield from the tranquilizer bullets. Lev wants desperately to return to his parents and be unwound, but Pastor Dan, his family's spiritual counselor, yells for him to run away with Connor.
Lev is accidentally hit by a tranquilizer dart. Connor carries him off the road. At the same time, a bus from a State Home swerves and rolls over. One of the passengers, Risa, is another teen set to be unwound. Although not a delinquent, Risa has no parents. As she has not been able to excel over others at the home in academics, sports or musical ability, Risa has been ordered unwound to make room for a new baby. Risa uses the bus accident to escape her fate and follows Connor and Lev into the woods.
Risa and Connor know they can't really trust Lev, but decide to keep him with them anyway, as they can't believe anyone truly wants to be unwound. When they come to a town, Connor hears a baby crying. He knows the child has been "storked," abandoned on someone's front steps. The homeowner is now responsible for the child unless the mother can be found. Years ago, Connor's family was storked. Instead of keeping the baby, they kept it inside the house for the day and then storked another neighbor. A week later, the same baby was left on their doorstep, only now it was very ill and soon died. The entire neighborhood attended the funeral. Connor realized that the baby had been passed around with no one to care for it until it finally died. He can't let that happen again, and so he approaches the homeowner who then insists he and Risa take the child.
Risa, Connor, Lev and the baby follow a group of teenagers onto a school bus. They hope to escape between leaving the school bus and entering the building, but they can't. They hide out in a girls' bathroom. Without Connor and Risa knowing, Lev ducks out and heads for the office. He tells the secretary that he's been kidnapped by two unwinds. She calls the police. He then uses the phone to call home.
Pastor Dan answers. He tells Lev that his kidnapping was never reported to the police. The authorities believe he's been tithed. Pastor Dan convinced Lev's parents to see the incident as God's providence. Lev begs the pastor to tell his parents that he wants to be tithed, but Pastor Dan won't do it. Lev realizes the pastor never believed all the platitudes he taught about the value of being a tithe. He wants Lev to escape and live a full life.
Lev is devastated by the knowledge that he'll be the cause of Connor's and Risa's unwinding. He flees the office and pulls the fire alarm. Connor and Risa are lucky enough to encounter a teacher willing to help them. As everyone exits the building, the teacher sends them to an antique shop in town and tells them to ask for "Sonia." Lev tries to catch up with them as they escape so he can apologize, but the crowd of students prevents him.
Sonia, the owner of the antique shop, runs a safe house for unwinds. They are kept in a hidden cellar until they can find transportation to another safe house. Connor, Risa and the baby spend a week in the dark basement with three other unwinds — Mai, Roland and Hayden. Hayden's parents divorced, and since neither parent wanted the other to have custody of him, they chose to have him unwound. Roland, a muscular teen with disciplinary issues, beat his stepfather in an attempt to protect his mother. His mom, however, took her husband's side of the fight and signed Roland's unwinding papers. Mai's parents kept having children until they got the boy they truly wanted. Since they couldn't afford to raise all six children, Mai was scheduled to be unwound.
Unable to sleep, Hayden tells the unwinds' favorite urban legend, the story of Humphrey Dunfees. Humphrey's unstable parents decided to have him unwound but then changed their minds after their son's body had been redistributed. Mr. Dunfee worked for the government and was able to track down the recipients of his son's parts. He and his wife supposedly killed them and tried to put their son back together.
Several days later, Sonia calls each of the teens upstairs, one at a time. She has them write a letter to someone they love. They are to write what they want the person to know, should they die. Sonia keeps the letters for a year after the teens turn 18. If they can keep from being unwound, they are to return and take back the letter. If they don't return, Sonia mails it.
The next day, the kids are shuttled to another safe house. The teacher who helped Risa and Connor offers to adopt the baby. Risa and Connor spend the next few weeks bouncing between houses until they end up with about 100 other unwinds in a warehouse.
Lev meets a teen nicknamed CyFi. CyFi is Umber, the name now used to describe a dark-skinned person. He speaks in an archaic urban dialect that used to be prevalent before the Heartland War. CyFi tells how after an accident, he received a full frontal lobe transplant from an unwind. CyFi is traveling to Joplin, Mo., but Lev doesn't know why. He decides to go with CyFi. One day, CyFi starts walking and talking differently, as if he's another person. Lev nervously follows him as CyFi enters a store selling Christmas items and steals an ornament.
Afterward, CyFi runs to a playground and cries. He smashes the ornament and then tells Lev to empty the pocket of his coat. Inside, Lev finds a treasure of stolen gold and diamond jewelry. CyFi insists he didn't steal the items and that Lev must hide them somewhere. Lev buries all but a diamond bracelet, and the boys continue their journey. Lev pawns the bracelet for money. He comes to realize that CyFi is being influenced by the brain transplanted in his head.
CyFi's unwind must have come from Joplin and is trying to get back home. CyFi tells Lev that the other boy, Tyler, didn't seem to realize that he was unwound. CyFi can hear his thoughts inside of his own head, and sometimes they overwhelm him. When they arrive in Joplin, Tyler directs them to his former house, where the police, his parents and CyFi's are waiting for him. Tyler is allowed to go into the backyard where he digs up a box of buried stolen items. He gives them to the police and then begs his parents not to unwind him. Distraught, Tyler's parents are speechless until Lev insists they put the boy at ease and promise not to unwind him. In the resulting reunion, Lev makes his escape.
Soon after Christmas, Risa, Connor and the other unwinds are packed four into a crate. The crates are loaded onto a plane and delivered to The Graveyard. Unfortunately, four boys die from suffocation. Connor and Risa survive the journey and settle into their new lives. The Graveyard is a place where decommissioned planes are sent. The Admiral, an older military man, runs the graveyard. The children live in the abandoned planes and everyone has a job. Risa ends up in the medical clinic while Connor becomes a maintenance man. The Admiral fears someone is trying to undermine his authority within the camp and so takes Connor into his confidence. Five of the Admiral's top teen aides were murdered. Connor tries to find out who did it. Connor suspects Roland, but doesn't have the evidence to prove it. Lev arrives at the camp, but does not want to reconnect with Connor or Risa. His time with CyFi and being alone have hardened him. He joins up with the group conspiring against the Admiral. It is not led by Roland, but by the Admiral's personal pilot, Cleaver.
Mai also joined with Cleaver, as her boyfriend was one of the teens that suffocated in the plane. Cleaver recruits Lev, Mai and another boy for a mission away from the graveyard. They will be injected with a special explosive, infiltrate a harvest camp, and blow up the harvesting facility.
Although Roland is not working with Cleaver, he is trying to take over the graveyard. By spreading rumors that the Admiral is running a "chop shop," selling unwinds to the highest bidder or using their body parts for himself, Roland is gaining a following.
Connor traps Roland in one of the transportation crates and questions him about the murders of the aides. Meanwhile, the other unwinds start a riot and try to attack the Admiral. When they can't get him, they beat Cleaver to death. Connor arrives to stop all-out anarchy, but the Admiral has suffered a heart attack. The only one who can fly him to a hospital is Roland. Connor releases him from the crate and he, Roland and Risa take the Admiral to the hospital. Roland betrays them and all the unwinds in the graveyard to the Juvey-cops, hoping to get a reward for their capture. His plan backfires when the cops tell him they've known about the graveyard for years but allow it to exist as it helps keep homeless unwinds from living on the streets and becoming criminals.
Roland, Risa and Connor are sent to a harvest camp to be unwound. It is the same camp that Lev has infiltrated. Before Risa and Connor can be unwound, Mia and the other terrorist blow up the facility. Lev does not detonate himself. Instead, he helps the injured teens to safety and willingly turns himself into the police. He is visited in his cell by Pastor Dan, who explains that Lev's actions have changed the face of the unwind industry.
A law has already passed changing the age limit of unwinding to 17. Risa is left paralyzed by the explosion, but refuses the transplants to heal her as then she could be unwound at a later date. Handicapped people can't be unwound. While Connor is in a coma, he's given transplants for his amputated arm and injured eye. When he wakes up, he is horrified to learn that his arm came from Roland. Risa assures him that he controls it now. Connor is given the identity card of one of the harvest camp's dead guards so that he can escape unwinding. The authorities are told that he died in the explosion. The Admiral refuses a heart transplant and so is no longer capable of running the graveyard. Connor and Risa take charge of saving the unwinds.
The Admiral returns to his home. He and his ex-wife are the parents on whom the legend of Humphrey Dunfees is based. They were forced to sign their son, Harlan, over for unwinding. The Admiral has contacted all the recipients of his son's body over the years. On what would have been his son's 26th birthday, the Admiral gathered them all together at his ranch in Texas. As the people mingle, they begin sharing memories they have of Harlan. Finally, the Admiral calls his son's name, and all the people turn to him. One calls him "dad." The Admiral and his wife welcome their "son" home.