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They take Rex to the infirmary.
Eli tells his mother about the night before their ninth birthday. He had told Eddy about a surprise that led him to hide in the range rover. Eli had known that Eddy would get sick because of his allergies and the proximity to the kitten. Then Eli would be the only birthday boy. This is why Eli has always blamed himself for what he thought was Eddy’s death. He apologizes to his mother, but she tells him that children make mistakes.
Eli breaks into his father’s office with an axe. He can’t find a way to switch on the Internet. He returns to the infirmary, hoping that Rex will be conscious and that he will tell him how to get online.
Rex’s temperature has dropped and now and he has diarrhea. Eli gets a medical diagnostic book from the library and reads about his father’s symptoms. He believes he has ergotism, from eating ergot-infested flour. His mother had allowed Rex to eat the flour, hoping it would only make him sick, but would not endanger him. Rex is awake enough to tell them that he has an antidote for ergotism. He has the antidote because, if taken in too large a quantity, it results in cyanide poisoning.
Rex begins to spasm, but he tries to give them the code for the door, reciting them as quickly as he can. He can’t get all the numbers out. Before he becomes unresponsive, he says the word “turducken” (186).
Eli’s mother says that Rex told her he would leave a clue to the code.
As he goes to search for clues, Eli finds Lexie in the kitchen, cutting Cara’s hair. Cara is another one of the Supplements. Lexie is trying to keep to her routine, hoping that it will help her feel normal. Eli asks if she will give him a haircut as well. He gives her clippers and asks her to buzz it all off. When she asks why, “There wasn’t an explanation I could put into words” (191).
Eli’s mother faints and starts bleeding while looking for clues in the secret lab.
Eli’s mother says that the doctor told her that Terese should have been her last baby because of complications. Rex let her get pregnant even though he knew this. Eli leaves her to figure out what Rex meant by the “turducken” clue he gave before he passed out.
Eli and Lexie tell Terese she was right about Rex, and that they now know the truth. Eli runs on the treadmill and tries to think of clues that will help him figure out the code to the hatch. He remembers one Christmas when they had Turduckens: a chicken inside of a duck inside of a turkey.
Lexie remembers when the Turduckens arrived. Rex had been excited and had told her that they had a mystery inside. Eli searches Rex’s office for more clues but finds nothing. He runs into Terese outside of Rex’s office and sees that she has been crying. He apologizes for always being a bad brother to her, and he says that he loves her, even though he hasn’t always shown it.
Together, they visit the Supplements. They find the word hautbois in the nesting doll that Lucas showed him earlier. The French word translates to “high wood,” but when said it loud, it sounds like the word “oboe.” Eli finds a scrap of blank paper in Lexie’s oboe case. He then pours ammonia on the paper, which reveals numbers written in invisible ink.
Rex comes into the room and congratulates Eli. Eli runs away, makes it to the silver door, and begins inputting the code. Rex follows him with Lucas and threatens to kill the boy if Eli doesn’t give up. Eli gives him the paper with the code.
Eli tried to memorize any numbers he could before giving the paper to Rex. He writes the numbers he remembers on a chalkboard. The numbers are all dates from nuclear attacks, something he wouldn’t have known if Rex hadn’t educated him so thoroughly on nuclear history. The code works at the silver door. He reaches a hatch at the top of some stairs but it’s closed. Rex appears behind him and grabs him. Eli kicks Rex down the stairs, and he and Lucas make it through the hatch.
Eli looks at the sky with Lucas. The light from the hatch goes out. The door is closed.
A helicopter lands near Eli and Lucas. Phil is the pilot. He raps on the hatch door and Rex opens it. Rex says they are going to an island he bought, to a new Compound. Phil has a detonator that will blow up the underground Compound when they are airborne, so that no one will know they were ever there, or that it ever existed. Eli hits Phil and accidentally begins the countdown to the explosion. They have ten minutes to get everyone out.
Everyone manages to escape, but when the family is together, they realize that they don’t know where Rex is. The Compound explodes. More helicopters, this time carrying a group of agents from the FBI land. Eddy gets out of one of the aircraft and hugs Eli.
After the rescue, Eli reunites with Gram. He learns the story of how Rex faked the family’s death while being questioned by the FBI. There is still no sign of Rex’s body.
Eli’s mother gives birth to a baby she names Finnegan. For their first week home in Seattle, their house is surrounded by news reporters. The tabloids invent stories about the family that are even crazier than the reality. To escape, the family takes a chartered jet to Hawaii, where they stay at Gram’s house. Eddy and Eli spend most of their time on the beach, teaching Cara, Lucas, and Quinn about the world.
Phil reads a statement on TV that says that the company was left to him in Rex’s will, but Eli’s mother says that she intends to play a prominent role in the company’s future.
While playing on the beach, Eli sees a half-empty Tums wrapper in the surf. Rex used Tums constantly while he was having stomach distress. Eli is nervous and rejoins his family.
The final chapters show the family escaping from the Compound, and from Rex, but there is every indication that they may be escaping from one prison into another. Chapter 21 and the Epilogue both make it clear that Phil and Rex always intended to move the family to another Compound. If Rex is still alive, then the danger that he will abduct and move the family to another Compound will always be present.
These chapters contain less philosophizing and become a rapid-fire sequence of events as the family bands together to escape from Rex. Ironically, the family bonding that Rex envisioned the family experiencing in the Compound does not take place until they unite against him. Eli’s conciliatory gestures to Lexie, Terese, and the Supplements make them feel as though they are a family, not just a group of people stuck together in a bunker.
Rex has always been a manipulative, sinister figure, but his indifference to the welfare of his family is concretized in the final chapters. He threatens Lucas, who is his son, to get Eli to give him the paper with the code. Even though doctors told Eli’s mother that having more children after Terese would be unsafe, Rex continued to impregnate her, knowing that it could result in her death, or the need for an emergency Cesarean delivery in the Compound. He ensured that he had a way to dispose of the family—and himself—via cyanide poisoning if he ever deemed it necessary. But his plans extended even beyond the current Compound. Rex has further experiments in mind, which will continue in the second book of the series.
At the end of the novel, the family is more emotionally close than the reader has seen yet, but the foreshadowing of the Tums wrapper—and the existence of another novel in the series—make it unlikely that their time in Rex’s experiments is over.