Four plot lines emerge: an autistic young school-bus driver named Danny decides to take his bus on his rounds one more time; an ex-military sniper named Kittridge holes up on a high floor of a Denver apartment building and begins shooting virals; Lawrence Grey, a janitor from the complex that Project Noah began in, wakes up in a hotel only to find himself younger and slimmer than he used to be; and Horace Guilder (a dying federal government functionary) copes with the country falling apart around him.

Meanwhile, Grey encounters a disoriented pregnant woman, who does not realize the dissolution of society around her, shopping for paint for her baby's bedroom in an abandoned Home Depot.

Danny and company drive to a stadium outside of Denver that was designated as a rescue site only to discover it full of thousands of dead bodies.

Kittridge and company, with the help of Major Frances Porcheki, arrive at a refugee site just outside the research center.

Grey manages to escape after apparently killing Suresh, a medical examiner, and Nelson before taking Guilder hostage.

By midnight, they travel to the camp by an underground waterway; Tifty, being the leader, sees water rushing through the vents and yells for them to run away.

Satch Dodd, the youngest survivor of the Massacre of The Field, in which his whole family was murdered, joins Peter at the mess hall.

Alicia Donadio has tracked down the home base of Julio Martinez, one of the Twelve, and leads an operation only to find him gone and only his familiar, Ignacio, who is also a janitor from Project Noah left behind.

Peter is immune to her powers, much to her surprise, and the ambush goes poorly for both parties when one of the convoy members explodes a fuel truck.

The city is run by Guilder, who is surviving along with Lila Kyle (revealed to be the hypnotic woman) by draining blood from Grey, who has been chained in a basement for 100 years.

The city is run by "redeyes," who are fed blood from Grey to keep young and healthy, and "cols" (collaborators), who serve as cruel enforcers.

Meanwhile, back at the military city in Texas, Amy and an imprisoned former-Colonel Greer escape and head to Iowa.

Peter, Michael, Lore, Hollis (Sara's boyfriend from the first book), and a black marketeer named Tifty, who was at the massacre of the field, head out to Iowa close behind.

Amy will present herself as "Sergio" and, when Guilder holds an elaborate execution and brings the entire town to watch, the resistance will be able to strike.

[4] BookPage wrote that the ending to The Twelve was more satisfying than that of The Passage, but that "there are plenty of loose threads to keep readers eager for book three".