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.

Jeremiah and Kurdy make their way towards Thunder Mountain, hoping to find whoever Simon was working for.

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.

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.

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.

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.

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 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.

The wanderer Jeremiah comes to the market community Clairfield, looking to barter for supplies and maybe get a lead on the whereabouts of the Valhalla Sector. The place is run by the beautiful Theo, a woman obsessed with getting her hands on as much knowledge and technology as possible. When her guards discover a well-maintained, fueled car hidden nearby, she's sure the owner can lead her to the jackpot. Pity those who should get in the way.

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.

Yet more questions and few answers, Mister Smith is here yet he is not. Kurdy is scared yet fearless, Jeremiah is weak yet strong. we see a father and son reunited only to be thrust apart. we learn more about Valhala Sector and their evil plans.

While held captive at Valhalla Sector he briefly meets the military people there and is introduced to the president and Jeremiah asks "President of What".

Kurdy is still not speaking to Jeremiah. Marcus sends Jeremiah and Libby(since she is the only one who knows the people there) to a camp where the members of the St. Louis gathering. Libby reports back and Kurdy leads the attack on the camp. They rescue everyone, but the leader escapes and heads east to find the mysterious Daniel. Marcus leaves Jeremiah in charge of the camp and the nearby village.

Markus struggles to achieve consensus among the factions that could re-build the country. He sends Kurdy with a new partner to rescue some of the delegates who have fallen into very tough hands.

Jeremiah prepares for an awkward reunion with his father, Devon. Libby gives Jeremiah a letter from his father written years ago. In it he explains what happened the day he and his wife disappeared.

While Kurdy tries to unravel the mysteries that surround Mister Smith, Jeremiah has a "High Noon" encounter with the citizens of Milhaven when some of Daniel's disciples storm into town.

Adam comes to Milhaven to kill Jeremiah and nearly succeeds, sending Jeremiah, Kurdy and Mister Smith on a dangerous mission into one of Daniel's strongholds.

Thunder Mountain is bringing new towns into the Alliance, drawing Daniel's attention and bringing Mister Smith a vision too awful to contemplate.

Wanting to savor his dish of vengeance while it's hot, Jeremiah joins Markus and Kurdy in a sting to smoke out Daniel's raiders. In Milhaven, Mister Smith gives Erin a disquieting message from God.

God tells Smith that he, Kurdy, Jeremiah, and Marcus will each be granted one miracle if they turn up at the appointed place at the appointed time. Smith is confident of a miracle but the others are more concerned with the growing threat of Daniel, and the army Kurdy is building.

Was the past the best of times or the worst of times? It depends on whose past. Kurdy has to trust Lee when he returns to a town and a load of trouble he left behind while Jeremiah is imprisoned in an idealized replica of the days before the Big Death.