As the spiritual powers of Ben Hawkins evolve, the entity Management reveals it's identity to Ben, (the Russian soldier in Ben's dreams) and then exposes him to a vision of the cataclysmic disasters (a nuclear explosion) that awaits the world if Ben doesn't identify and conquer his nemesis: Brother Justin, the creature of darkness. In order to do this, Ben must find his father, the elusive Henry Scudder, who holds the knowledge of the preacher's identity and location. In the aftermath of the fire whichhuged Apollonia, Samson covers for Ben by claiming that he died in the fire to get rid of the Texas Ranger still hanging around the troupe, and Samson helps Ben hide the dead body of Professor Lotz, while Lila becomes concerned for the missing Lotz well being. A distraught Sofie runs away, leading a guilt-ridden Jonesy to assemble the carnies to go out looking for her. Meanwhile, Brother Justin's radio sermon has employed two new 'apostles'; an occultist named Wilfred Talbot Smith, who aids Justin that he musthug Henry Scudder to become a true immortal, and a prison inmate named Varlyn Stroud whom is also 'called' by the mesmerizing Justin's voice. Reporter Tommy Doyle continues to investigate the Chin's ministry fire, while Justin and his sister Iris use the radio to continue to spread the word, drawing throngs of weak and impoverished masses into their spiritual web, while Reverend Balthus suffers from a stroke.

Ben travels on his own to Alamogoro to seek out Father Kerrigan, a former preacher residing in a lunatic asylum, and who knew his father who tells him to beware of a mysterious tattooed man that both Ben and Brother Justin see in their dreams. Back at Carnivale, Stumpy continues his pursuit of Rita Sue and Libby's well being by gambling. Ben finds a distraught Sofie wondering on the road and brings her back to the troupe, while nobody realizes that although Sofie's mother is dead, her ghost (whom only Sofia and see and hear) still lingers around her. Still worried about the missing Lotz whereabouts, Lila looks through his trailer and finds that he couldn't have left at all. Sofie's comes to a decision about where she stands with Carnivale by doing some manual labor, which upsets the other men in the company. Meanwhile, Stroud breaks out of prison to begin his mission for Brother Justin. In Mintern, Justin and Iris start to make groundwork on the location of his latest ministry, the Temple of Jericho, while Dolan continues investigating the Dignity Ministry fire. Also, Justin starts paying late-night visits to Mintern's Chinatown, to a tattoo artist...

When Carnivale sets up show in Ingram, Texas, Ben sets out to find some people who knew Scudder and stumbles into a bizarre moonshiners camp which proves both painful and revealing. Meanwhile, Stroud continues his quest to find Scudder by investigating the mining accident in the ghost town of Babylon. At Carnivale, Sophie still refuses to read Ben's future through the tarot cards, but the cards soon reveal something without Sofie's assistance. Ruthie's luck with her snake charming skills seem to be turning against her. Stumpy pitches Rita Sue and Libby to an underage audience, and he later gets a visit from a menacing bookie looking to collect. In Mintern, Tommy Dolan continues his investigation into the arson incident, while Brother Justin takes the catatonic Reverend Balthus under his wing, as well as takes advantage of his young and naive new housekeeper, Celeste.

Still held captive in the moonshiners camp, Ben meets his blind and elderly grandmother who reveals some family secrets and a mysterious face of passing. Meanwhile, Lila confides in the rest of the riggers that she suspects Samson was responsible for Lotz demise. Jonesy instructs Sofie to dig a large hole in the ground. In Mintern, Justin continues his mesmerizing evil sermons to his Temple of Jericho congregation where he has a seizure when he has a vision of the threat that Ben poses to him. In Los Moscos, New Mexico, Stroud reports his progress to Justin who advises him to turn his search to looking for Ben Hawkins. Iris tries to cover-up her own secrets from Dolan while imploring Justin not to keep secrets from her. Ruthie continues to see visions of the diseased Lotz and Apollonia, while Stumpy's moneymaking schemes begin to wear on Rita Sue and Libby.

When the Carnivale stops outside Creed, Oklahoma, they receive an uninvited visitor: Varlyn Stroud who begins asking questions to Jonesy, and later to Samson, about where to find Scudder. Meanwhile, Rita Sue bails out Stumpy for his 0 gambling dues, but he bets (and loses) all of the money on a big fight anyway. In Mintern, Justin pushes Dolan to make a decision while Iris confesses to Dolan about being the one responsible for the ministry fire. Back in Creed, Ben pays a visit to an elderly mask-maker for information about Scudder, which turns into a literal nightmare. Ruthie confides in Sofie about her visions of seeing dead people, including Lotz and Apollonia. Sofie also finally reads tarot cards for Ben who thinks he finally knows where to find Scudder. At the end, Justin receives a mysterious gift: a passing mask of himself and when he puts it on... he sees Ben.

On the road to Damascus, Nebraska, Samson and the troupe stop to help when they run into a rival troupe that has fallen on hard times. In Mintern, Dolan tries to help Iris and Justin find a solution to their legal problems while Iris is surprised when she learns of Justin's real plan: to frame Dolan for the ministry fire. Back at Carnivale, Rita Sue learns that Stumpy lost all of their money with gambling while he and Jonesy come to blows over Rita Sue. Ben and Sofie decide to explore their growing romantic relationship with sex when she tells him that she intends to leaves Carnivale and wants him to come with her. Also, Ruthie appears to have a psychic connection with Lotz when she briefly speaks in his voice to Lila. Also, Ben finally decides to go on ahead towards Damascus when he learns from Sampson about Stroud who's on Scudder's tail.

When Carnivale finally arrives in Damascus, Ben gets closer to finding his father when another vision of a man with the shredded face leads him to the town's seedy hotel. Ben then goes to investigate further, and finally meets his father, who is working as a clerk at the hotel. Meanwhile, Bishop McNaughton arrives at Brother Justin's new residence at the Temple of Jericho at New Canaan where he puts Justin on notice about the content of his sermons. Back at the Carnivale, Jonesy cannot get the departed Sofie out of his mind, while Libby and Rita Sue continue their war of words. With Ben unaware that Stroud is on his trail, Ben learns more about who he is when he brings Scudder to Management. He learns that Scudder is Management's evil opposite. Also, Libby and Jonesy finally 'get it on' over their growing attraction to each other.

Ben and Samson have a heated argument over some bad news that Ben tells him about the passing of Management, and Samson learns from Ruthie about seeing Stroud abduct Scutter. Ben suggests that they must track down Stroud at once so he will lead them to Brother Justin. Meanwhile, Iris and Justin back a local politician while Justin reveals his evil side to Reverend Balthus. Back at Carnivale, Rita Sue tries to play hardball with Bud, Stumpy's debt collector, by showing him who's the boss. Libby shocks her parents by revealing that she and Jonesy got married after a drunken night out, which prompts Stumpy to stage a dinner with them. In New Canaan, Wilfred Talbot Smith arrives with more bad news that he's interpreted a bad sign for Justin that his enemy has the power to destroy him with a special dagger. Lila offers to support Ruthie over her recent emotional status. At Carnivale, Jones is blamed for an accident when a car on the Ferris wheel collapses, and Ben resorts to draining the life force from a young woman to save the life of her son. At the end, Sofie finds a new job: as the new house maid for Brother Justin.

While driving down a desolate highway in rural Utah on his trail of Stroud, Ben comes across Jones and Libby, the victims of a vigilante group blaming Jonesy for the Ferris wheel accident, leading to Ben to try to heal Jonesy. Back at Carnivale, Ruthie has another possession by the deceased Lotz who leaves a lipstick message that Sofia is the Omega. Lila then tries to reach the deceased Lodz. At the Canaan camp, the invalid Reverend Balthus takes a shot at Justin during his fiery political sermon, and when chaos breaks out, Justin shocks the crowd with forgiveness. Meanwhile, Iris takes Eleanor on a picnic where she makes the mistake of confining in Iris that she suspects that Brother Justin is actually a demon, and Iris pays her back by revealing that she already knows... and thenhugs her. Sofie finds salvation in her new work for Brother Justin. On the road, Stroud lets the morphine flow for the captive Scudder, while Ben tries to get a head on Stroud's whereabouts.

Following another one of Ben's visions, he and Joney set out to find Stroud and they soon arrive in the Wyoming state capital where from a discarded newspaper in a recently vacated hotel room, they finally learn the name and location of Ben's nemesis. Back at Carnivale, Libby struggles to stick to her alibi that Jones concocts for them, but lets the story about Ben slip to her mother. Samson then has a heart-to-heart talk with Libby about Ben's magical abilities. At Justin's ministry camp, Stroud arrives and finally meets his evil master face-to-face. There, Wilfred Talbot Smith intercepts a near disaster for Justin and reneges on a deal with Scudder, who plans an escape... but Justin does a little backseat driving. Also, Iris discovers that Sofie is actually Justin's illuminate daughter, while Stroud increases security for Justin.

When Samson announces that the carnival's next stop is in the Christian camp of New Canaan, California, both Lila and Stumpy challenge his authority. Jones arrives back with the troupe and gives Samson the information what he and Ben found about Brother Justin. Meanwhile, Libby urges Jones to reveal the secret of Ben's powers to the rest of the troupe, despite Samson's protest. While Ben infiltrates Justin's ministry camp to look for him, he finds Sofie being baptized as a new converts when a new tragedy rises from the pond... in the form of the cuddled Eleanor. Later, Justin is startled by a development in the migrant camp when Samson and Jones arrive and persuade Iris to let them set up shop there. That night, when Ben wants to make his move tohug Justin, Jones intervenes and urges patience.

Samson devises a grand plan by scheming with Ben, Jones, and the entire troupe to lure Brother Justin to Carnivale for his confrontation with Ben. Meanwhile, Stroud wants to protect Justin who correctly suspects that the carnival is setting a trap for him. Sofie finds herself locked in a dark shed after she tells Justin her conflicted thoughts about where her loyalties lay, and soon becomes terrorized by ghostly visions of her mother. Rita Sue is touched by Samson's generosity of giving her the money needed to pay off Stumpy's loan shark. Later, the final confrontation approaches when Brother Justin persuades Iris to overcome her fear of heights by riding the Carnivale Ferris Wheel where Jones traps both of them in for Ben to drain Justin's powers, and Ben performs his most important healing of Reverend Balthus, leading to Ben and Justin finally meeting face-to-face, and the visions of Ben and Justin becoming full circle. At the same time, Joney sets out to rescue Sofie from Stroud, but soon realizes (way too late) that she has made her choice to which side her loyalties are.