After a young man named Ben Hawkins buries his mother on the grounds of his family's repossessed farm, he's taken in by a traveling carnival on its way to a stint on the outskirts of yet another impoverished Dust Bowl town. Ben's shackles and strange spiritual powers worry a blind mystic named Lodz, but the carnival's day-to-day manager, the diminutive Samson, insists that Ben remain. The decision irks head-rigger Jones, who senses there's chemistry between Ben and Sofie, a tarot-card reader whom Jones fancies. Meanwhile, in Mintern, California, an evangelical preacher named Brother Justin receives a "sign from God" that leaves him shattered and amazed - and awakened to the possibilities of his own mysterious powers. Back at the carnival, Ben debates whether or not he should remain with this bunch of "freaks" - but an unforeseen inspiration keeps him in the fold.
A practical joke by Jones leads Ben to a piece of the puzzle that is his past. Meanwhile, Brother Justin and his sister Iris (who lives with him in Mintern) are going through their own changes. Most notably, Brother Justin is attempting to turn Chin's, a Chinese brothel, into a house of worship for migrants - but he must convince the brothel's skeptical owner to make the deal. At the carnival, Sofie tends to her comatose psychic mother, Apollonia, after she has an upsetting run-in with Ben.
When authorities of the cash-poor town of Tipton refuse to let the carnival set up, Samson takes Jones' advice and temporarily reinvents the troupe as a religious-revival show - with Ben as its headliner "act." Brother Justin is headlining his own new show at the former Chin's, promising to bring "Old Time Religion" to migrants, a move that upsets his regular congregation. Back in Tipton, Ben and Sofie visit an ailing woman outside of town in search of clues about his history. At the last minute, Samson decides to change Carnivàle's travel itinerary from north to south.
On the road to Babylon (Texas), the carnies come face-to-face with nature's fury. Lured by clues about his past, Ben reluctantly follows Lodz into an abandoned house, where the seer tests Ben's powers; Sofie socializes with a handsome café owner, to Apollonia's chagrin; Samson pays a visit to an old flame, a prostitute named Jolene; and Jones, facing a roustabout mutiny, comes up empty in his effort to meet with Management. Meanwhile, Brother Justin struggles with an ultimatum: give up his new migrants' ministry at Chin's, or face losing his old congregation at First Methodist.
As Brother Justin tries to make sense of a major catastrophe, the carnival rolls into Babylon, a tapped-out silver-mining town with a luckless history - and few visible inhabitants. Samson looks to raise morale by treating the troupe to a night at a local bar in town, while Sofie and her new friend Libby (one of the cooch dancers) take in a film. A drunken Ben falls down a mineshaft, where he unexpectedly encounters a familiar face. Finally, a group of restless miners arrive just in time for the evening cooch show - and the latest tragedy to befall Carnivale.
Thirsty for payback, the carnies get caught up in an obscure yet fascinating phenomenon known as "Carnival Justice." Ben's dark adventure ends, and Lodz is there to welcome him back into the fold. Meanwhile, Brother Justin decides to take a trip - destination anywhere - and ends up wandering in the wilderness. Later, he swaps campfire stories with a group of hobos, one of whom is about to change Justin's life.
While Brother Justin rediscovers his "birthright" on the banks of a river, his sister Iris gets some unexpected support from an attentive radio reporter. At the carnival, Rita Sue and Stumpy argue over their family's future; Ben and Ruthie go hunting for snakes to use in her act; Samson goes to work on the bally; and Libby and Sofie see stars on the western horizon.
Samson sends Ben on a road trip to enlist a new attraction, where he encounters a longtime carney rival named Phineas Boffo. Sofie debates whether to defy her mother and join Libby on the bally; Stumpy tells Jones he needs to get his “candle waxed”; and Lodz and Samson have a falling out over Ben’s errand. Meanwhile, while Brother Justin is receiving treatments for “religious excitation,” Tommy Dolan is posing a rallying cry for his radio listeners: "Where are you, Brother Justin?"
Ben tries to stave off the torments of his dreams by staying awake, but the lack of sleep is taking its toll. Samson looks to drum up new business by resurrecting several tried-and-true scams, including “turtle boy” and “man eating chicken”; Lodz warns Ben about the dangers of not practicing his “gift”; Sofie worries that her mother is losing touch with reality; Ben marvels at Ruthie’s snake-charming routine; and Lodz’s psychic act gets a jolt from a mysterious source. In Mintern, Iris reaches out to Brother Justin over the radio airwaves, and Tommy gets a surprise reaction when he reaches out to Iris.
Brother Justin returns to Mintern to chart out a new direction for his ministry. At the Carnivàle, Samson’s loss is Lodz’s gain; Libby catches on to her mother’s deception; Sofie accuses Apollonia of “breaking the rules”; Ben and Samson come up empty in search of information about Scudder’s whereabouts; Stumpy takes his lumps in enlisting a new dancer named Catalina; and Lodz and Lila wait for Ben to finally succumb to sleep.
With Management’s blessing, Lodz hatches a devious plan to “reach” Ben, who is vulnerable after letting his guard down with Ruthie. Rita Sue upstages Catalina in the Gay Paree tent; Sofie reads Stumpy’s cards and doesn’t like what she learns; and Ben learns that some wounds aren’t easy to heal. In Mintern, Balthus is concerned about the influences surrounding Brother Justin, as well as some fiery allegations that Tommy Dolan threatens to make public. For her part, Iris proves she’ll do anything to advance her brother’s career.
Faced with a crisis of life-and-death proportions, Ben turns to Lodz for advice, and ends up meeting with Management for the first time. Stumpy and Rita Sue strike a deal with each other, and Jones, to save their marriage; Samson covers for Ben when the law comes knocking; and Sofie settles a score with Libby and Jones, only to find herself in the grips of Apollonia’s fury. Meanwhile, Balthus and Brother Justin contemplate the former’s "greatest evil," with the latter pondering the prospect of salvation versus damnation among his congregation: "The clock is ticking, brothers and sisters... counting down to Armageddon."
As Brother Justin spreads his radio message to the weak and huddled masses, his word reaches the ears of a new "apostle" - prison inmate Varlyn Stroud - and occultist Wilfred Talbot Smith, who pushes him to seek out the elusive Henry Scudder. Meanwhile, Management also urges Ben to find his father, showing him visions of the apocalyptic horrors that otherwise threaten. Tommy Dolan does some sleuthing on the Dignity Church arson; Reverend Balthus is stricken ill; and Lila worries about Lodz's whereabouts. Meanwhile, Samson does his best to quell suspicions among the troupe.
Stroud hits the road on his mission, making rapid progress. Ben seeks out a former associate of Scudder's named Father Kerrigan, a disturbed artist whose "vision" Ben has seen before. Justin and Iris welcome a beautiful new "servant" into their home. Meanwhile Samson threatens to replace Stumpy, who works Rita Sue and Libby harder than ever; Sofie seeks comfort in manual labor, to the men's chagrin; Lila challenges Samson's easy dismissal of Lodz; Management confides in Ben a secret fear; and Justin makes another late-night visit to Chinatown.
As Ben searches for a mysterious next link, Justin tends to his flock. Meanwhile, Stroud investigates a mining accident that left all but one man dead; Sofie refuses to read Ben's tarot but the cards have an agenda of their own; Dolan grills another arson witness; Ruthie is visited by a mysterious shadow; Stumpy peddles the girls to a barely legal audience; Gabriel assists Ruthie in her latest death- defying act; and Ben receives a rough welcome when he stumbles upon distant relatives.
A relative of Ben's reveals to him dark family secrets - and the face of death. Stroud reports on his progress to Justin, who now sees the threat Ben poses; Balthus bears witness to more of Justin's abuse of power; and Iris beseeches Justin not to keep secrets, though she's desperate to protect her own. Meanwhile, Burley wants to do business with Rita Sue, as Stumpy ponders an even more distasteful scheme to feed the local hungry men; Lila finds a wealth of clues in Lodz's trailer; Ruthie continues to see visions; and Libby dances around the tension with Jonesy, who gives Sofie a new assignment.
Justin is pushed by Dolan to make a difficult decision; Iris gives an important dictation; Ben has a nightmare visit with a mask-maker; Ruthie shares her visions with Sofie, who decides to help Ben; Rita Sue is generous with Stumpy, who bets on a big fight; Libby fishes for a compliment from Jones; Stroud continues his pursuit of Ben; and Justin receives a mysterious gift that gives him a new perspective.
The troupe breaks bread with another carnival and Samson makes a deal with an old friend named Sabina; Iris and Justin prepare for their most difficult sermon yet; Stumpy panics as Rita Sue goes on a charity mission; Jones and Stumpy both try to defend Libby's honor; Lila makes a new friend; and Ben and Sofie dance around family issues.
Justin and Iris placate Bishop McNaughton with a hearty breakfast; Ben follows his visions to a seedy hotel with Stroud hot on his tail; Sabina airs her dirty laundry with Lila; Libby and Rita Sue do some self-reflection; Iris displays her strength to Norman; the troupe worries about Sofie; Libby gives Jones special treatment; and Samson is distracted while Management tries to destroy a gift from Ben.
Ben and Samson have a heated argument; Iris and Justin back a local politician; Rita Sue tries to play hardball with Stumpy's debt collector; Libby shocks her parents with an announcement; Ruthie seeks refuge in the safety of her trailer; Smith interprets a bad sign for Justin; Stroud nurses a wound; Jones is blamed for an accident; and Sofie finds a new job.
Ben and Jones learn that justice is "for the birds"; Ruthie's visitor leaves lipstick traces; Lila tries to reach Lodz; Sofie finds salvation in her work; Iris takes Eleanor on a picnic; Balthus misses a big chance; Stroud keeps the morphine flowing; and when chaos breaks out during a public speech, Justin shocks the crowd with forgiveness.
Libby struggles to stick to her alibi, buckling under the weight of Rita Sue's superiority; Jones goes for a ride with Ben; Ruthie delivers a nocturnal message to Lila; Talbot- Smith intercepts a near disaster for Justin and reneges on a deal with Scudder; Iris discovers a relative; Stroud increases security with his "Knights of Jericho," and Justin does some backseat driving.
When Samson announces the carnival's next stop, Lila challenges his authority; Stumpy and Rita fear dark days to come; and Libby urges Jones to reveal a secret to the troupe. As Justin baptizes his converts, a new tragedy rises to the surface; Ben volunteers to stack firewood; Sofie sees a face from her past; Iris welcomes a chance to sponsor some fun; and Justin is startled by a development in the migrant camp.
As the world grows smaller, Samson devises a grand plan; Justin forces Iris to face her fear of heights; Stroud wants to protect Justin; Sofie finds herself in the dark; Rita Sue is touched by Samson's generosity; Ben performs his most important healings.