_____Peter and Amy are on their way again, riding on Greer's horse. But when they reach a bridge across a river, all that's left of it is the beams, too narrow for the horse to walk across. So they send the horse away, after Amy silently communicates to it that that's what they want to do, and negotiate the narrow beams across the river.
Finally they reach the ruins of the compound, where first Amy and then Peter hears someone singing. They follow the sound to a small log house in a clearing in the forest, where they find Sister Lacey Antoinette Kudoto.
Meanwhile, Sara is tending to the wounded on the convoy and thinking about settling down in Kerrville with Hollis. The convoy halts when one of the trucks breaks down. Then one of the wounded soldiers wakes up and tells Sara about his bad dream of a fat woman. And Alicia returns from scouting ahead and tells Greer that they've spotted tracks: "The Many. And they're headed straight for that mountain."
Theo and Mausami have discovered that the farm had belonged to a family named Conroy, and they give the family's name to a starving dog they find in the barn. They bathe and feed the dog who settles in with them, but Theo suddenly realizes that the barn had been latched. How did Conroy find his way into it. So he goes outside to check and finds human footprints in the barn and an opened can that someone has eaten from.
When Lacey had left Amy and Wolgast, the viral who had attacked her was Carter -- who didn't so much attack as feed, communicating to her his sadness and the whole story of the death of Rachel Wood. She realized, "He was not like the others," and she gave him her blessing. She was rescued by Jonas Lear, who helped her heal and lived with her in the cottage they built from the ruins of the Chalet, the central building of the facility. Because he had given her the form of the virus that had been given to Amy, she didn't age; but he did, and she had lived on in the cottage for fifty-four years after his death until Amy and Peter showed up.
Lacey gives Amy her old Powerpuff Girls knapsack, with the remnants of what had been in it, including the stuffed rabbit. Amy shares her memories of Wolgast, and Lacey tells her that she had stayed behind, "So someone would be here when you came back." Jonas Lear had set up the beacon to call for her return. Amy tells them of the voices she hears from the virals: "They're so sad. They have such terrible dreams. I hear them all the time.... They're dying and can't stop. Why can't they stop, Lacey?" Lacey replies, "I think that they are waiting for you, to show them the way." Then Lacey brings out the file folders on the men used in the experiments.
Alicia is leading a party that consists of Michael, Sara, Hollis, and Greer, who relinquished his command of the convoy. Along the way they find the body of the horse Peter and Amy had sent back at the bridge.
Peter reads through the files and discovers that all of the subjects of the experiment, except Amy, had been criminals sentenced to death. When he reaches Babcock's file, he learns that Babcock had originally been from Desert Wells, and thinks, "They always go home." Lacey comes to him after he has read the files and tells him the story of Noah from the Bible. Peter is Noah, she suggests, the one who will see to it that the world is reborn, and when he asks, "if I'm supposed to be Noah, then who's Amy?" "'The ship, Peter,' said Lacey. 'Amy is the ship.'"
As he's thinking about this, Lacey looks startled, and Amy comes into the room. They have sensed that Babcock is on the way. And Lacey tells Peter it's time for him to see "The passage." They follow her to the south side of the mountain and down its side to a dark tunnel. Lacey opens a doorway and they are in a brightly lit hallway -- "Level Five," she says Lear called it. They go to what looks like an infirmary, where Lacey opens a cabinet and takes out a small metal box that contains "two rows of tiny glass vials, containing a shimmering green liquid. He counted eleven; a twelfth compartment was empty." It's the virus that Amy and Lacey were given -- Lacey's is the missing twelfth vial. Peter puts the box in his backpack, along with a handful of syringes.
Alicia returns to the group and tells them she has found tracks. They move forward through the forest, but then Michael hears a sound above him. A gun goes off and Michael is knocked off his horse. He sees a viral crouching a few meters away from him and hears gunshots and people calling his name, but he concentrates on killing the viral with his knife, which he plunges into its chest. Then Peter and Amy appear, and Amy administers the coup de grace with Michael's rifle, telling it "I'm sorry" as she does. Michael, Peter and Amy hear more gunfire and run toward it.
Lacey has tricked Peter and Amy into going ahead as she sets the timer on a small nuclear bomb, then closes the door, locking them out. She communicates to Amy, "You will know how to set them free, to make their final passage." Then she waits for Peter and Amy to leave and opens the door again, waiting for Babcock.
Peter, Amy and Michael reach Lacey's cottage; Sara, Alicia, Hollis and Greer are there already. They barricade themselves inside, but the virals quickly attack the cottage, breaking through the barricade, and one of them bites Alicia before Hollis can kill it.
Lacey, concerned that Babcock hasn't taken the bait and that the virals are passing her by, goes to the mouth of the tunnel and summons Babcock. She runs back into the tunnel, thinking of how her mother had told her to run when the soldiers attacked. Babcock follows her and the bomb goes off.
Amy is the first to stand up after the explosion shakes Lacey's cottage, and she leads Peter and the others outside, where the dazed virals, freed from Babcock's control, are standing. She walks among them, communicating their old names to them, as the sun rises and begins to kill them. Peter joins her, and she tells him to go inside and save Alicia. He gives Sara one of the vials and a syringe, and when she protests that she doesn't know what it is, he tells her, "It's Amy."
The injection doesn't have much immediate effect, and they begin to worry about the lack of supplies and the oncoming winter, as well as the effects of the radiation from the bomb. When it seems that the Amy virus is not working and that she is about to turn, Peter orders the others out of the room. He has promised Alicia that he'll be the one to kill her in such a case, and he crouches over her with the knife aimed at her breastbone.
Mausami goes into labor. It's prolonged and difficult, but she finally gives birth to a boy they name Caleb. Exhausted, they all fall asleep, except when Conroy awakens Theo to be let outside. But when Theo wakes up again, Conroy has vanished. Theo goes to look for him and finds the dog dead. Then he hears Mausami scream and races back to the house to find it empty. He hears her scream again and finds her in the barn, in the back seat of the old Volvo that was stored there, clutching the baby. The creature attacks him, knocking the shotgun he is carrying out of his grip and flinging him against the car. He lets the viral attack him, not wanting to see what it would do with Mausami and the baby.