The story unfolds in three “Books”: “The 13th Apostle”/“The New Messiah”/”The Crucifixion”, title-lettered Ten Commandments-style.
A struggling Hebrew man in A.D. 33 Jerusalem, Clarence, and friend Elijah lose a chariot race with Mary Magdalene (and money the victory would have brought) due to difficulties such as gypsies shooting darts at them, and almost running over a dirt-encrusted beggar, Benjamin.
Clarence owes money to loan shark Jedediah the Terrible, but also loves Jedediah’s sister Varinia. Roman soldiers racially profile Clarence and Elijah for a theft they didn’t commit.
Clarence, a marijuana smoker who steals honey wine from the Romans, smokes opium one day, around the floating-in-air bodies of other opium-smokers, and, seeing a light over his head, conceives the idea of being a fake messiah, capitalizing on the rise of Jesus Christ, to free himself of debt and start a life of glory. John the Baptist slaps him for being a hypocrite when he drops by to be baptized.
Clarence proposes to the Twelve Apostles that he become the 13th apostle. They laugh at him. Clarence’s blue-eyed twin brother Thomas, one of the Twelve, is cynical and dismissive towards Clarence. In turn, Clarence criticizes Thomas for leaving their mother to follow Jesus.
Judas Iscariot proposes that Clarence free a group of gladiator slaves, to earn his place as an apostle. Clarence goes to the gladiators’ owner and proposes he free them. The owner instead says he’ll free the slaves if they beat Clarence to death; then says he’ll just have the huge Barabbas the Immortal fight Clarence.
Clarence wins through trickery; Barabbas is freed, and goes with him. Barabbas is rebellious against Roman rule and antagonizes Roman soldiers. Barabbas claims to be truly immortal, except if hit in the heel (like Achilles).
Clarence visits Jesus’ mother Mary, and father Joseph, asking how he can perform the same “tricks” Jesus does. The parents insist that Jesus is real, not a trickster.
Clarence, Elijah, Barabbas, and Zeke travel the land, with Clarence performing “miracles” like bringing Elijah “back from the dead”. They make much money. Also, Clarence, an atheist, preaches “knowledge over belief”. However, Clarence decides to use the money to free the gladiators, rather than paying back Jedediah.
Mary Magdalene is being stoned to death due to accusations of sexual congress with Romans. Elijah tries to shield her. Jesus arrives, stops the stones’ flight in mid-air, and notes that the stone-throwers are themselves sinners. He heals Mary’s wounds. Elijah believes.
Varinia betrays Clarence by being at a party with him, with Jedediah waiting outside. Jedediah tries to collect his money, with Romans helping him. Barabbas resists, though Clarence insists he run away.
Barabbas is speared three times, but survives, killing a Roman centurion sent after him. Jedediah is impressed and makes up with Clarence, though the Romans take Clarence away, since they are supposed to arrest any messiahs.
Pontius Pilate interrogates Clarence, who confesses that he is a trickster, not a messiah. Pilate says that despite confessing to fraud, Clarence may save himself by walking across water (a nearby pool). Clarence, to his own amazement, is able to do so, following a vision in the clouds. Nevertheless, Pilate says he will crucify him.
Varinia visits Clarence in prison, and kisses him. Thomas also makes up with him. Pilate mocks Jesus’ ideas of human equality, though Clarence mocks the Romans’ male nude statues.
Jesus gives money to Benjamin, and the ability to multiply coins. The newly-rich Benjamin buys a “makeover”: under the dirt, he is a long-haired white man who resembles conventional portrayals of Jesus. Benjamin traipses around, throwing money to people, and Romans believe he is another “messiah”.
On the way to the cross, Amina, Elijah, and Barabbas watch. Cabbage, a small gypsy who despised Clarence, now helps carry his cross. Benjamin is crucified alongside Clarence, complaining that an onlooker is making a painting of him (looking like a traditional white Jesus).
Jesus tells his weeping disciples that he himself will be betrayed and crucified. Jesus comes to Clarence’s tomb, forgives his prior unbelief, and raises him from the dead and heals his nail wounds. Clarence now both “knows” and “believes”, and smiles.