After an engineered virus called Captain Trips lays waste to the world, a few people with immunity to the virus survive and converge on the State of Colorado in the US.
In the desolate New York City, Larry meets Rita, and the two set out to flee the city. As the convict Lloyd is trapped in a prison where he's the only survivor, he receives an unexpected visit from Randall Flagg.
Back in her childhood, Nadine is contacted by Flagg via a Ouija board, while, in the present, she finds the child Joe, and the two meet Larry. Stu finds Frannie and Harold but is unable to join them due to Harold's jealousy. The deaf-mute Nick spurns Flagg and decides to go to Mother Abagail.
As the Boulder Free Zone Committee seeks to strengthen their rule and sends out spies to try and get the measure of Flagg, the latter carries on with his machinations to undermine them and nip the emerging society in the bud.
Flagg tries to pressure Danya into revealing who the third spy is, while Nadine desperately seeks a way to be freed from Flagg's control. Suspicious of Harold, Stu and Frannie devise a plan to find out what he's up to. Mother Abagail invokes God's counsel.
As Mother Abagail goes missing, the residents of Boulder start to worry, so they form search teams to find her, unknowingly enabling Harold and Nadine to carry out a wicked plot. Meanwhile, Flagg is joined by the maniacal Trashcan Man.
In the aftermath of Nadine and Harold's plot, they flee Boulder to join Flagg in New Vegas, while Mother Abagail calls on members of the Committee to embark on a life-or-death mission.
In New Vegas, as the Boulder citizens meet Flagg's minions in a final showdown, Nadine turns up looking very different.
As Frannie gives birth to a baby girl whom she calls Abagail, she's left with a tough decision to make on which hangs a lot.