In the future, the pro-life/pro-choice debate became so heated that it resulted in a second American civil war. After years of brutal fighting, the two sides signed the Bill of Life which stated the following: 1. All life is protected from conception to the age of 13; 2. Between the ages of 13 and 18 a parent could choose to retroactively unwind a child. Unwinding involved systematically dismantling a person for organ/limb transplant; all parts are used, and all are kept alive, so technically the life of the Unwound was not put to an end. At the start of the novel, Unwinding was an accepted part of life.

Connor Lassiter, 16, was prone to get into fights at school. As a result, his parents decided to have him Unwound. After discovering this, he decides to run away with his girlfriend (who is not an Unwind). When the time comes, she does not leave with him. Risa Ward, 15, is a ward of a state home(Ohio StaHo 23). After making a few mistakes during her classical piano recital, she is sentenced to being Unwound due to budget cuts. Levi (Lev) Calder is a tithe. As the youngest of 10, his parents had him for the sole purpose of tithing 10% of their children to charity. He is having a party on his 13th birthday to celebrate the culmination of his life's purpose. His oldest brother Marcus refuses to participate and is disowned by the family.

Connor gets the help of a trucker, but the Juvey cops track him using his cell phone. They are stopped on the side of a highway, and Connor flees across multiple lanes of traffic. He grabs Lev (also on his way to the Harvest Camp to be tithed) out of a car as a hostage. The bus containing Risa crashes to avoid the commotion, and Risa races of into the woods. Lev is hit by a tranquilizer, but not before his Pastor (Dan) is able to tell him to run. In the woods, Connor overpowers a Juvey cop and shoots him with his own tranquilizer gun.

The next day they come across civilization. Risa tricks a woman out of food. They are spotted by a cop, so they head towards a bus stop. As they arrive, they hear a boy claim they have been storked (anyone is able to leave a baby at another person's doorstep. If they get away without being seen, the baby becomes the legal obligation of the home owner) again. Connor (remembering a time when he said the same thing when their neighborhood had illegally passed a storked baby around until it died) takes the baby from the doorstep. He, Risa, and Lev are then forced to board the bus to avoid the cop.

At school they hide in a girls bathroom. Lev slips away and turns them in. When he realizes what he has done, he pulls the fire alarm to help Connor and Risa escape. They do (with the help of a teacher who sends them to a member of the Unwind underground railroad), but not before they see Lev calling their names. They assume (both correctly and incorrectly) that he has betrayed them.

In the underground, they meet Hayden, a sarcastic rich boy, Roland, a manipulative bully, and Mai, a goth. Eventually they arrive in The Graveyard - a decommissioned plane graveyard where an ex-Navy Admiral protects runaway Unwinds until they are 18. We learn Connor's escape from the Juvey cops is the stuff of legend (he is the Akron AWOL). Connor becomes close to the Admiral, while Risa works as a nurse. Roland builds a network of power to overthrow the Admiral. Lev, meanwhile, helps Cyrus Finch (CyFi) track down the parents of an Unwind who he received a piece of brain from. CyFi still has memories of the Unwind. Lev arrives at the Graveyard a few weeks later, now bitter and angry.

Lev falls in with a group of Clappers (terrorists who turn themselves into bombs). A riot erupts in the Graveyard (due to the discover death of 5 Unwinds at the hands of the Clappers) and the Admiral becomes gravely ill. Connor, Risa, and Roland fly him to a hospital and Roland turns them in. They are taken to a harvest camp. Lev arrives shortly after with the other Clappers (Mai is one as well). Roland is Unwound. Mai and the other Clapper destroy the chop shop just as Connor is taken inside. He loses an eye and an arm. Lev leads the rescue of those injured by the explosion, thus choosing not to clap himself, and eventually confesses to the police.

Connor receives Roland's arm, and he is given the false identify of a nineteen year old. Risa is wheelchair bound. Lev's decision not to clap puts a face on the anti-Unwind movement and changes begin to occur. The legal age is reduced to 17. Connor, Risa, and Hayden take over the Graveyard. The Admiral recovers, but not fully (he refuses Unwind transplants). We also learn he is the parents of the infamous Humphrey (real name Harlan) Dunfee. After he was unwound, his parents spent their lives trying to piece him together. They did so by gathering everyone who got a part of him. At his 26th "birthday party" all these people gathered together and, for a moment, their collective consciousness came together and "Harlan" was there.

Lev will go to live with his brother Marcus. Connor will lead the new Unwinds in the Graveyard in an effort to free as many Unwinds as possible, at least until the Unwinding is put to an end permanently.