Oklahoma Dust Bowl, 1934. 18-year-old Ben Hawkins is a young man whom lives with his physically sick, God-fearing mother. After his mother dies from a long illness, Ben unceremoniously buries her in the back yard of his home which is then repossessed for outstanding late payments. Ben is taken in by a traveling carnival troupe (titled Carnivale) and becomes acquainted with the residents whom include the kind-hearted dwarf owner Samson; his right-hand man and head rigger Clayton Jones; Gypsy tarot reader Sofie; the bearded lady Lila; girlie tent owner Felix 'Stumpy' Dreifuss, his wife Rita Sue whom Felix solicits to some of the patrons, and their two teenage daughters Libby and Dora Mae; Gekco the Reptile Man; snake charmer Ruthie; Ruthie's son Gabriel, the low-IQ strongman; and conjured twins Alexandria (Alex) and Caladonia (Cat). Ben is revealed to have strange mystical powers of clairvoyance and healing which worry Professor Lodz, the blind mystic of the traveling troupe. Meanwhile in the small town of Mintern, California, an evangelical preacher, named Brother Justin Crowe, receives a sign when a woman vomits up silver coins that disappear before his eyes, that leaves him awakened to the possibility of mysterious powers that he has and it somehow gives him a psychic connection to Ben, both of whom have never met.

A practical joke which has him clean an old dirty trailer leads Ben to a piece of the puzzle of his past - a tuxedo-clad man named Scudder who Ben keeps seeing in his dreams and who may be his long-lost father. Meanwhile, Brother Justin and his sister Iris have a conversation with Justin's mentor, Reverend Norman Balthus, which makes him realize that he has a gift that he must put to use. With the help of a vision that comes to him at the right time, he persuades the owner of the local brothel Mr. Chin's to allow him to turn it into a house of worship for the local migrants. At the Carnivale, Sofie continues to tend to her comatose, telepathic mother, Apollonia, after their upsetting run in with Ben, whose powers can help, or harm.

When the authorities of the cash-poor Oklahoma town of Tipton refuses to let the carnival set up show, Samson takes Jones' advice and temporally reinvents the troupe as a religious-revival show with Ben as the center act of a healer. In Mintern, Brother Justin's promise to the migrants of their new church upsets his regular congregation whom despise the seedy people. Meanwhile, Ben and Sofie team up to continue to search for clues about his mysterious past when they meet with an ailing old woman outside Tipton who knew Henry Scudder, Ben's father.

On the road to Babylon, Texas, the carnival encounters a horrific dust storm, called a 'black blizzard'. Intrigued with clues about his past, Ben follows Lodz into an abandoned house where the seer tests Ben's powers. Meanwhile, a lonely Sofie socializes with a handsome cafandeacute; owner. Samson visits an old flame while Jones, facing a roustabout mutiny of the carnies, comes up empty in his effort to meet with the mysterious and godly Management which controls Carnivale. In Mintern, Brother Justin struggles with an ultimatum by Reverend Norman Balthus: give up his new migrants ministry at Chin's, or face losing his old congregation at First Methodist.

The carnival finally arrives in Babylon, a tapped-out silver mining town in rural Texas with few inhabitants. Samson tries to improve the troupe's spirits with a night of revelry at the local bar while Sofie and Libby (one of the chooch dancers) get closer and decide to attend the local cinema. Eventually, a group of restless miners arrive in time for the chooch show, but with drastic consequences when they start a riot. Meanwhile, Ben has an enlightening experience at the bottom of a mineshaft where he has a vision of the mysterious Scudder fighting in the trenches of World War I.

Thirsty for payback after the cuddle of Dora Mae Dreifuss, one of the chooch dancers, Samson and the rest of the carnies, including Stumpy Dreifuss and Rita Sue, get caught up in an obscure, but fascinating phenomenon called 'Carnival Justice' to root out the person responsible. Meanwhile, Ben's dark adventure in the mine shaft ends where Lodz welcomes him back into the fold. In Mintern, Brother Justin, highly distraught over the mysterious fire that destroyed Chin's andhuged six homeless children, leaves the town and wanders in the wilderness, where he meets a group of hobos around a camp fire where one of them is an undercover reporter.

While Brother Justin rediscovers his 'birthright' on the banks of a river, Iris gets some unexpected support from an attentive radio reporter, named Tommy Dolan, whom offers to spread the word about Brother Justin's parish. At the carnival, Rita Sue and Stumpy argue over their family's future where she, afraid that the family will end up on the breadline, argues with Stumpy over leaving the carnival and moving to Hollywood. Meanwhile, Ben and Ruthie go hunting for snakes to use in her act, and Ben is forced to use his powers to heal Ruthie's simpleton son, Gabriel, after he injures himself, at a cost of several dead fish. Also, Samson goes to work on the bally, and Libby and Sofie see stars (and romance) on the western horizon.

Samson sends Ben on a road trip to enlist a new attraction, where Ben encounters a longtime carnival rival named Phineas Boffo. Back at the carnival, Sofie debates whether to defy her mother and join Libby on the bally of the chooch tent. Meanwhile, Stumpy tells Jones he needs to get his 'candle waxed' and offers to set Jones up with Rita Sue. Lodz and Samson have a falling out over Ben's errand in which the old mystic turns to the mysterious Management. In Mintern, while Brother Justin is committed to a lunatic asylum and 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. Meanwhile, Samson looks to drum up new business by resurrecting several tried-and-true scams, including 'turtle boy' and 'man eating chicken'. Lodz warns a distrustful Ben about the dangers of not practicing his 'gift'. Sofie worries that her mother is losing touch with reality after she has a vision about her father raping Apollonia. Ben marvels at Ruthie's new 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 who's still in the asylum, and Tommy gets a surprise reaction when he makes a pass onto Iris.

Brother Justin returns to Mintern from his stay in the asylum to chart out a new direction for his ministry. At the Carnivale, Samson's loss is Lodz's gain when the blind mystic takes Samson's place as the liaison to Management. Libby catches on to her mother's deception of her lustful fling with Jones, while Sofie accuses Apollonia of 'breaking the rules' when she forces Sofie to tell the truth to their tarot clients about their bleak futures. Ben and Samson come up empty in search of information about Scudder's whereabouts when they visit one of Scudder's hangouts; a men's club called the Templars Club. Stumpy takes his lumps in enlisting a new dancer, a Mexican waitress named Catalina, whom he runs into during a drunken bender in the troupe's New Mexico town. Also, Lodz and Lila wait for Ben to finally succumb to sleep, with a little of Ruthie's help, so Lodz can probe Ben's dreams.

With Management's blessing, Lodz hatches a devious plan to 'reach' Ben, who is vulnerable after letting his guard down after his night of seduction with Ruthie. Rita Sue upstages Catalina's debut routine in the Gay Paree tent. Meanwhile, 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, Reverend Balthus is concerned about the influences surrounding Brother Justin, as well as some fiery allegations that Tommy Dolan threatens to make public that the fire that burned down Chin's was an inside job. For her part, Iris proves she'll do anything to advance her brother's career and reveals that she was the one responsible for the fire in order for Justin to turn to his dark side.

Faced with a crisis of life-and-passing proportions of whether or not to cure Ruthie from a snake bite, Ben turns to Lodz for advice, and he ends up talking with the mysterious and unseen entity, Management, for the first time. Meanwhile, Stumpy and Rita Sue strike a deal with each other, and Jones, to save their marriage. Samson covers for Ben when a Texas Ranger comes looking for Ben in which Samson learns that Ben is a fugitive for a cuddle charge which he did not commit. Sofie settles a score with Libby and Jones by seducing Libby in order for Jones to find out after learning that he's been seducing Rita Sue. But the consequences are when Sofie finds herself in the grips of Apollonia's fury for this sapphic act. In Mintern, Reverend Balthus and Brother Justin contemplate the former's "greatest evil", with the latter pondering the prospect of salvation versus damnation among his congregation.