Jeremiah and Kurdy are captured by Michael and his men, who operate out of a local military base. Michael has concluded that God is dead, and it's about time someone took his place... by any means...

While trying to track down info on "the Burners", a mysterious group that's burning down whole settlements in seemingly random fashion, Jeremiah encounters a woman who's stealing all the gas she can get her hands on, and Kurdy ends up helping a pregnant girl, against his better judgment.

The son of a medical doctor has set up what may turn out to be a dubious medical practice of his own, traveling with his brother from town to town and exploiting people...and finds that his past catches up with him.

Jeremiah and Kurdy travel in search of more information on the Big Death and Valhalla Sector, and along the way discover some potentially dark secrets about the fate of Kurdy's parents in the last days of the Big D.

Kurdy and Jeremiah find a recon team in enviro suits and capture one prisoner...Quantrell, who commanded Thunder Mountain before the Big Death, when Markus and his father worked there as well. While Quantrell is enigmatic about where he came from, Markus flashes back to when his mother arrived at the quarantined military base and Quantrell left her outside. Markus' father insisted on going out to be his wife, exposing the base. Quantrell escaped to Valhalla Sector. Quantrell's people are tracking him by an implanted GPS tracker and Quantrell warns that now his people are going to emerge an take over. Meanwhile, Lee is apparently working for someone else and lets the enigmatic Ezekiel in to Thunder Mountain. Ezekiel first meets Jeremiah and claims they are brothers.

Jeremiah and Kurdy attempt to save a community when its children begin disappearing amid a rumor that the blood of children can be used to prevent the return of The Big Death.

Jeremiah and Kurdy befriend a group of people dedicated to nonviolence who are searching for what they call a New World. While the pair thwart the group's takeover by a band of ruthless and cunning thieves, it is ultimately the misguided group's own leadership that may lead to their undoing.

Kurdy and Jeremiah goes to Clairfield to save Elizabeth who has been kidnapped by some of Theo's former underlings. In Thunder Mountain there is an investigation trying to find the traitor who is leaking information.

Jeremiah and Kurdy arrive in Mayfair and find the townspeople dead of cyanide. In the next town of New Hope they find the locals have an aversion to touching. The Elders ruthlessly enforce the law, making anyone who disobeys their edicts "disobey". When the people they befriend start disappearing, Jeremiah intervenes and is taken away where he finds out the offenders are stoned to death. Both towns are an "experiment" in determining how the original virus was transmitted, and the Elders destroyed Mayfair when they "failed". Jeremiah and Kurdy break free and expose the Elders' scheme to the unsuspecting townfolk. Meanwhile, back at the base Marcus takes ill from an undiagnosed disease and begins suffering hallucinations of a Native Indian - Lee pushes the matter before the Council to determine the line of succession and fails.

Jeremiah and Kurdy are sent to contact an elusive group led by a mysterious "Steve" but get captured. One of his captors is Michelle, a woman he met (in flashback) back at his empty home five years ago after his brother died. They were intimately involved back then, and we find out she's the one who gave Jeremiah the idea for writing notes to his dead father. In the present it turns out "Steve" is Michelle. Her operation is working heavily to get knowledge out, and she also has a 5-year old son. One guy accuses Michelle of skimming and the guys follow her and find out she's collecting art, and agrees to work with Thunder Mountain. Then Michelle comes back to lay down the law on the guy who accused her of skimming and the guys head out with as Jeremiah and Michelle think about getting together in the future.

Realizing that Valhalla Sector is systematically taking control of the Nuclear Missile Silos starting from the east coast and moving east to-wards Thunder Mountain (Cheyenne Mountain) Marcus decided to make their Presence Known at a nearby town that has a missile silo, they offer men machines electricity and medicine, in hopes of winning over the people of the town and make an ally of the people so they can stop the advance of the people of Valhalla sector, but Ezekiel appears and is seen by Jeremiah talking to Chen, suspecting something wrong he chases after Ezekiel but is knocked out by Chen from behind, when Jeremiah wakes up he runs to warn Marcus that something bad is going to happen when he is struck down by a snipers bullet fired by Ezekiel in a nearby building.

After receiving a message from Theo (from "The Long Road") saying she wants to "thank" Jeremiah and Kurdy for saving her life, they find themselves wrapped up in a world of sex, bare knuckled boxing matches, elephants, and mushrooms? After they arrive at the inn specified in the invite (after taking some hallucinogenic mushrooms), they find it's a cathouse and they've been given the run of the place. Jeremiah's "choice", Penny, wants him to fight in a bare-knuckle match for her freedom but Kurdy overhears that it's a plan to get revenge on Theo by killing them and takes Jeremiah's place. Kurdy manages to win and Polly has them take her to her daughter China at...a local circus (which explains the elephant). While Polly tries to deal with the fact her child's father doesn't want her to have contact with her child, Jeremiah helps recover the elephant and Polly decides to stay on as the circus decides to "go public".

Kurdy and Elizabeth try to make contact with an isolated "black power" movement, while Erin drags Jeremiah along to help get her twin sister out of trouble.

Kurdy and Jeremiah are off to Jeremah's old stomping grounds of Denver to pick up some books at a library. They meet the "librarian", Edgar, and Kurdy stays to help him learn to read and fend off zealots who are convinced that books are the root of all evil. Jeremiah goes to meet his friend Red (from The Long Road) and embarks on a journey with his girlfriend Maggie, a wheelchair-bound woman determined to deliver her father's ashes to the remote island where she was raised. Maggie insists the ashes must be dumped in the middle of a river...which can only be reached by a rickety gondola. Meanwhile, the library patrons rally under Kurdy's inspiration to defend Edgar and the library.

Markus's position as Thunder Mountain's leader is challenged by brothers who are threatened by the decision to introduce outside community leaders to the secret headquarters.

Jeremiah and Kurdy discovers that someone is a traitor, this leads them to the missing page in Simon's diary. With the help of the diary they find the real reason behind the Big Death.

Erin and Markus goes to St. Louis to hold a conference in an attempt to better the world. Jeremiah does not heed Ezekiel's wishes and visits Milhaven, hoping to find the truth about his father.