The story mentions that this novel is the continuation of the last novel's plot, The Passage, before introducing us to Danny, Kittridge, Lawrence, and Horace. Danny is a school bus driver who misses driving around the kids. He is autistic, and he loved his job. Kittridge is a military person who lives in Denver. He is a trained sniper, when the post-apocalypse began, he survived by killing all violent trespassers from a long way off. Lawrence is a janitor who used to work in a Project Noah complex, but one day, he mysteriously wakes up and he's younger and healthier than he was when he went to sleep. Horace Guilter is a defunct government employee who languishes the downfall of the government.
Then the story zooms in on Danny. He finds two 18-year-olds, April and Tim. They join him, and eventually, they meet Kittridge. Grey falls in with a woman named Lila. Kittridge and company find a clan of survivors, and Lawrence finds himself abducted by a man called Guilder. He is transported to a lab. At the group, Kittridge meets Major Porcheki, who clues him a plot: the government (what it's left of it) is waiting for the "virals" to invade the city (like zombies), then they will destroy the whole city.
We flash forward to see a clan of families about 75 years later. They have a picnic in the sun, because zombies don't come out in the light. We learn that Curtis feels Tifty is to blame for letting his brother Boz die. We flash backward a few years to learn about Curtis and Tifty. They were children together, and they were part of the same friend group, and Tifty didn't tell Boz that water was coming through a pipe he was in, so he got pinned by the water to a grate and died. Back 75 years in the future, at the picnic, they are ambushed by virals who massacre the clan. There is a human witch among the zombies who enchants children and takes them back into the woods with the zombies.
5 years after the plot of the first novel, we learn about Amy. She lives and works at an orphanage on a military base. She is visited in her dreams by Wolgast, so she agrees to find him to clarify the message from her dream. We meet Peter Jaxon, a battle-hardened soldier from the war against the virals. The remainder of survivors includes Julio Martinez who is part of a secret group called The Twelve. They seek to recruit the rest of the members.
One a trip to get oil back to the base, Peter encounters the witch again. He is immune to her psychic tricks, and when an explosion happens, they all escape to see a new day. Alicia finds a city run by Guilder, the man who kidnapped Lawrence from the beginning. He has been chained in the basement for 100 years, but he has retained his sanity. Lila Kyle is revealed to be the witch. We learn about a girl named Sara who lives in a city of low income residents in "concentration camps."
Guilder has decided to exploit The Twelve for the health regeneration, and he plans to enslave them. In the resistance, a woman named Alicia is raped and tortured by his men. Sergio decides to give himself up, so the resistance can ambush them while they are executing Sergio in the town square. That Lila woman wakes up from her long daze and lights flammable potions, exploding the basement where Lawrence has been tied up. Wolgast, the man from the dream, kills the master virals with a bomb, and Amy is turned into a viral. Alicia waits for Zero, the first viral, and plans to kill him.
