The story opens with Barabbas at the edge of those who gathered to be with Jesus as he was crucified. Barabbas was himself condemned to die but because of the Passover, the people were allowed to set someone free. Given the choice between Barabbas and Jesus, the people allowed Barabbas to go free. He would later be called "Barabbas, the acquitted," and would be condemned by many of Jesus' followers. When Barabbas is unshackled and told to go, he somehow finds himself following the three men who are to be crucified up the hill to Golgotha. He knows one of the thieves being executed, but says that he doesn't look at that man, only at Jesus.

After Jesus is dead, Barabbas notes that he's taken away carefully and entombed. Barabbas then heads to Jerusalem where he meets the Hare-Lipped Woman, a witness to Jesus' resurrection who will later be stoned for sharing her Christianity. After her death, Barabbas carries her lifeless body many miles to entomb her in a grave with her stillborn child. As it happens, the woman had once taken care of Barabbas when he was injured.

When Barabbas enters Jerusalem after witnessing Jesus' death, he is immediately caught up with friends who are amazed that he is alive. They are skeptical of Barabbas' claims of a holy glow about Jesus before he was taken to his death and about the darkness on Golgotha at the moment of his death. Barabbas eventually buys into their explanations and decides that it must have been tricks of his eyes because of his recent time in the dark dungeon.

Barabbas spends days shadowing the Christians, seemingly thirsting for knowledge, but never quite accepting. He has become an indifferent thief and eventually leaves the band.

He's later enslaved and spends years in a copper mine, shackled to a Christian man named Sahak. Sahak shows Barabbas that he has the mark of Christ on the back of his slaves' medallion and scratches the marks into Barabbas' medallion as well. Barabbas prays with Sahak at first, then unaccountably stops. An overseer questions Sahak about his religion and eventually arranges for Sahak to leave the mines and work in the fields. Sahak refuses to go without Barabbas and the two men are moved.

There comes a time when another slave notes Sahak praying and questions him about his religion. Sahak shows the mark of Christ and the slave apparently informs the overseers. The Roman governor calls for Sahak and Barabbas and questions them about the mark of Christ on their medallions. The governor points to the front of the medallion that proves the two men are property of the state. Sahak insists that he belongs to Christ and Christ alone. Barabbas says that he allowed the inscription because he wants to believe. Sahak is executed but Barabbas is moved into the governor's home as a slave. When the governor moves to Rome, Barabbas is taken along.

In the slaves' basement quarters of the Roman home, he sees the sign of the fish and begins looking for the slave who might be a Christian. He overhears two talking about a meeting of the brotherhood and slips out to watch. He doesn't find the meeting but returns to the city to find houses being burned all over town. Thinking that the Christians have started the fires, Barabbas joins in and claims to be working for Jesus. He's captured and imprisoned with true Christians who are guiltless but are to be crucified anyway. Barabbas is crucified alone and his dying words are, "To thee I deliver up my soul."