The story begins in Gethsemane in medias res as Jesus prays and is tempted by Satan, while his apostles, Peter, James, and John sleep. After receiving thirty pieces of silver, one of Jesus' other apostles, Judas Iscariot, approaches with the temple guard and betrays Jesus with a kiss. Peter cuts off the ear of Malchus, but Jesus heals the ear. The temple guard arrest Jesus and the apostles flee. John tells Mary and Mary Magdalene of the arrest, and Peter follows Jesus at a distance. Caiaphas holds a trial of Jesus over the objection of some of the other priests, who are expelled from the court.
When questioned by Caiaphas whether he is the son of God, Jesus replies "I AM", which to Caiaphas justifies the charge of blasphemy, and Jesus is condemned to death. Three times Peter denies knowing Jesus, and the remorseful Judas returns the money. Tormented by demons, Judas flees the city and hangs himself with a rope from a dead donkey. Crows fly down and peck his eyes out, and eat them.
Caiaphas brings Jesus before Pontius Pilate to be condemned to death, but after questioning Jesus, Pilate sends him instead to the court of Herod Antipas, as Jesus is from Herod's ruling town of Nazareth. After Jesus is returned, Pilate offers the crowd that he will chastise Jesus and will be set free. Jesus is viciously scourged but the people still demand Jesus to be crucified. Though, Pilate gives the people an option of freeing Jesus or Barabbas. When Barabbas is chosen, Jesus is sentenced to be crucified. As Jesus carries the cross along the Via Dolorosa to Calvary, Veronica wipes Jesus's face with her veil. Simon of Cyrene is unwillingly pressed into carrying the cross for Jesus. Jesus is crucified, and after his death, a single drop of rain falls from the sky. Jesus is lowered from the cross to his mother Mary, who looks directly at the audience in this Pietà. The movie ends with Jesus's resurrection and exit from the tomb, with the holes in his hands from the nails visible as he walks.