Nine years ago, the Detonations destroyed most of the world. All that remains is a domed city near Washington, D.C., and the struggling, disfigured and mutated people who live in the crumbling city outside the Dome. Dome-dwellers refer to people like Pressia and her grandfather as Wretches.
During the Detonations, many people, including Pressia’s parents, were killed. Those who survived became physically fused with people, animals or items that were near them. One of Pressia’s hands is now a doll head, and Grandfather has a fan lodged in his neck. No one outside the Dome is free of deformity, and many strange, dangerous creatures roam the area.
In the early days after the Detonations, the people in the Dome dropped messages saying they would help those outside. Help never came. The OSR, which once stood for Operation Search and Rescue, now means Operation Sacred Revolution. Its Wretch leaders rule by fear, and they hope someday to storm the Dome.
When Pressia turns 16, she is required to turn herself in to the OSR. She will either be used as a soldier, or if she isn’t strong enough to fight, target practice.
Partridge lives inside the Dome. He attends the Academy where he undergoes coding that fixes his imperfections. This is why those inside the Dome are known as Pures. His father is one of the leaders in the Dome. Partridge believes his mother is dead and that his older brother, Sedge, committed suicide.
Since Partridge lives in the dorms and doesn’t have a close relationship with his father, he’s surprised to be called in for a talk. His father questions him about some of the reactions recorded during his recent coding sessions and asks if his mother ever gave him pills. He remembers she did, but he keeps his mouth shut. He’s concerned by something his father says, referring to his mother in what seems to be present tense. He starts to wonder if she isn’t dead after all.
When a teacher takes Partridge’s class on a fieldtrip to the vault that holds the belongings of the dead, he looks through some items that were once his mother’s. His curiosity is further piqued, and he decides he must find out if she’s alive. He determines he can escape through the Dome’s air filtration system.
Partridge asks a girl named Lyda to the school dance, knowing she has keys to the historic display of kitchen items in the building. He takes her keys and steals a knife from a display. She catches him doing it, but allows him to pocket it without asking any questions. They dance and kiss, and he holds her hand as he walks her back to her dorm.
Soon afterward, he makes his escape during his coding session. After his escape, Lyda is locked up in rehabilitation for questioning in Partridge’s escape plot. At her mother’s urging, she tells the questioners that Partridge was in love with her. She hopes this will give her some leverage that may help her get out of rehabilitation.
Pressia inadvertently attends a meeting held by an 18-year-old conspiracy theorist named Bradwell. He says those in the Dome set off the Detonations to wipe out any who were imperfect in the world. Bradwell has live birds fused to his back. Pressia is put off by his arrogance. But when her 16th birthday arrives, she finds he’s left her a map that will lead her to his home if she needs help. The OSR is holding one of its bloody games, in which different teams get points for the number of Wretches they kill. She realizes she has to get away.
While looking for Bradwell, she sees some groupies (several people who have become fused into one person) drunk and trying to rob a boy. She can quickly see he is different, and she distracts the groupies so the boy can run. The boy is Partridge.
When Pressia is finally alone with Partridge, she can hardly believe she is talking to a real Pure. He asks her to help him find an old street on which he once lived, and she takes him to Bradwell’s house to get his help. Bradwell can’t believe Partridge’s naivety.
Partridge was always taught that an alarm sounded the day of the Detonations, warning everyone to enter the Dome. He believed those left outside the Dome had simply chosen not to come. Bradwell guides Pressia and the culture-shocked Partridge underground. An old woman confirms Partridge’s belief that his mother is still alive somewhere.
Readers meet a mid-level OSR leader called El Capitan. The young man’s job is to decide what happens to the new recruits. Those who can’t be used as soldiers are caged or killed or used as human test subjects. He’s sometimes ordered to hunt sickly recruits the way one hunts a deer.
El Capitan was riding a dirt bike with his brother at the time of the Detonations, so his brother, Helmud, is permanently fused to his back as though he’s carrying him piggyback. El Capitan sometimes gets angry and wishes he could kill Helmud, but he knows this would also mean killing himself. He has been ordered to bring Pressia in and put her in a leadership role.
OSR officers capture Pressia when she steps outside of Bradwell’s hideout. When Bradwell and Partridge realize this, they attempt to put aside their differences and focus on getting her back. It dawns on Bradwell that Dome leaders orchestrated Partridge’s escape without him realizing it. They had made everything he needed, such as blueprints and access to his mother’s belongings, readily available to him. They wanted Partridge to get out, and they are somehow using him to help capture Pressia.
Bradwell suggests there is no Operation Sacred Revolution, but that the OSR is actually working for the Dome. Bradwell smashes a necklace belonging to Partridge’s mother, and they discover an inscription in Japanese. Bradwell, who studied that language, says it means my phoenix. He says phoenix is the name of the operation Partridge’s father headed, where the intention was to detonate and destroy the planet so life could regenerate. Then the Dome dwellers would re-emerge to a better world, a new Eden.
The boys arm themselves and burn all of Partridge’s mother’s belongings. They leave the un-inscribed part of the locket, hoping Pressia will return, find it and know they’re looking for her.
In her new post at OSR, Pressia is taken to El Capitan. He explains she’ll have to kill a weak recruit. She can’t do it, and El Capitan puts the boy out of his misery. El Capitan’s boss, Ingership, then arrives in a car and takes Pressia for a drive. He shows her his home, an almost idyllic farm in the middle of the Deadlands, where he and his workers are trying to engineer food for the Dome dwellers. Most of what they’re making is still experimental.
Ingership introduces Pressia to his wife, who is covered head-to-toe in a body stocking. She pretends to love being domestic and feminine, as is expected of those in the Feminine Feminists movement. But when she gets Pressia alone for a moment, she slips her a note that begs for help. Pressia savors the food Ingership politely serves. She throws up in the end, because the experimental food is still indigestible.
Ingership shows her pictures of her grandfather being well cared for in a Dome hospital. If she wants to keep him this way, she must follow orders. She discovers Ingership is a liaison between her world and the Dome. He says the Dome allowed Partridge to escape because they are looking for his mother, who is alive and hiding on the outside. They want Partridge to find her, with Pressia’s help. Then Pressia and the OSR will return the mother and son to the Dome.
The driver of Ingership’s car returns Pressia to El Capitan. She is somewhat dazed. Using secret signals, she tells El Capitan the OSR is working for the Dome. El Capitan kills the driver. Then he and Pressia set out to find Partridge.
Partridge and Bradwell wander past former gated communities and burned asylums. They recall how the world had become increasingly full of insane people because of crime, government intervention, militant patriots and general emotional unrest.
Bradwell talks about his parents’ discovery that the Japanese had surrendered after Hiroshima because they were secretly experiencing mutations similar to the ones now occurring outside of the Dome. They were afraid the whole country would be affected, he says, and they needed help. Mutated housewives, many of whom are fused with their children, capture the boys. Bradwell hopes the women will take them to the legendary Good Mother so she can help them find Pressia.
Pressia waits in the car while El Capitan goes to Bradwell’s hiding place to look for clues and weapons. He finds the broken necklace. Beings that are partially human and partially earth, called Dusts, begin to attack Pressia. She and El Capitan fight them. She thinks she is about to die, and then she wakes up in the presence of the housewives and the Good Mother herself.
The Good Mother’s mutation includes a huge metal cross through her stomach, chest and neck and a still-breathing infant embedded in her upper arm. She says they’ve been watching for Pressia. Pressia is reunited with Bradwell and Partridge. The housewives refer to them, and all men, as Deaths. They say their men left them to fend for themselves after the Detonations. They want to know why Pressia is special to the Dome.
The teens aren’t sure. Partridge tells them about an old fairy tale called the Swan Wife, which his mother told him often. Unpacking the story, they discover Partridge’s mother was giving him a message. She had an affair with a Japanese man after leaving Partridge’s dangerous father.
The kids realize Pressia was the result of that affair, and that she and Partridge are half-siblings. The Good Mother says she will help the kids find their mother, if Partridge will give her his pinkie finger in return. Since they have nothing else with which to barter, they agree.
El Capitan joins them. After hearing Pressia’s story of visiting Ingership’s house, Partridge tells the group that he believes Pressia has a bomb implanted in her head.
Partridge’s father sends Lyda outside of the dome to deliver a message to Pressia. One of the supersoldiers takes her to the group, since the Dome has been tracking the kids from the start. The box Lyda gives Pressia contains the fan that was once lodged in her grandfather’s neck. It’s their way of letting Pressia know she shouldn’t have defied them.
After what Lyda’s seen, and after being with Partridge again, Lyda knows she can never go back to live inside the Dome.
Following patterns of light reflecting from Partridge’s mother’s necklace, they determine her location. Aribelle, his mother, is little more than a human head with a body made out of fused metals. Pressia is happy to meet her real mother at last. Aribelle says Partridge’s father is worried because Dome inhabitants are starting to deteriorate, due to a condition called Rapid Cell Degeneration.
Partridge and Pressia tell her they’ve discovered Sedge, whom they thought was dead, has been turned into a supersoldier. Aribelle briefly reunites with Sedge before a bomb goes off in his head. It kills him and badly injures Aribelle’s face. El Capitan gives Pressia a gun and urges her to kill her mother out of mercy. She does.
The group returns to Ingership’s house, demanding he remove the bomb from Pressia’s head. They learn that Ingership’s wife never actually activated the bomb. They kill Ingership. Each tries to determine his or her role for the future in the battle against the Dome.