Act 1

After a foreboding instrumental opening number ("Overture"), apostle Judas Iscariot expresses in musical monologue his concern over Jesus' rising popularity as a "king" and the negative repercussions that will have. He strongly criticizes Jesus for accepting his followers' unrealistic views and for not heeding his concerns ("Heaven On Their Minds"). While Judas still loves Jesus, he believes that Jesus is just a man, not God, and worries that Jesus' following will be seen as a threat to the Roman Empire which would then punish both Jesus and his associates. Judas' warning falls on deaf ears, as Jesus' followers have their minds set on going to Jerusalem with Jesus. As they ask Jesus when they will be going to Jerusalem, Jesus tells them to stop worrying about the future, since whatever will happen is determined by God ("What's the Buzz?").
Recognizing that Jesus is irritated by the badgering and lack of understanding from his followers, Mary Magdalene tries to help Jesus relax. Judas is concerned that Jesus is associating with Mary, who is presented (implicitly) as a prostitute in the musical. It seems to Judas that Jesus is contradicting his own teaching, and he worries that this apparent lack of judgment will be used against Jesus and his followers ("Strange Thing Mystifying"). Jesus tells Judas that Mary is with him (Jesus) now, and unless Judas is without sin he should not judge the character of others. Jesus then reproaches his apostles for being "shallow, thick and slow" and somewhat bitterly answers that not a single one of them cares about him. Mary Magdalene tries to assure Jesus that "Everything's Alright" while anointing him with oil. Judas angrily insists that the money used to obtain the oil should have been used to help the poor instead. Jesus sadly explains that he and his followers do not have the resources to alleviate poverty and that they should be glad for the privileges they have. He claims that once his followers no longer have him, they will lose their path.
Meanwhile, Caiaphas (the high priest), Annas, and other Jewish priests who have been studying Jesus' movements meet to discuss Jesus and his disciples. Jesus' growing following consists of Jews unwilling to accept the Romans as their rulers, and the priests believe that Jesus may become seen as a threat to the priesthood's integrity and the Roman Empire. If the Romans retaliate, many Jews will suffer, even those who are not following Jesus. Caiaphas tells them they are "fools" for not seeing the inevitable consequence of Jesus' activities. He believes there could be great bloodshed and the stakes are "frighteningly high". For the greater good, he has to "crush him completely, so like John before him, this Jesus must die". Annas and the other priests concur. ("This Jesus Must Die"). As Jesus and his followers arrive exultantly in Jerusalem ("Hosanna"), they are confronted by Caiaphas, who demands that Jesus disband them, which Jesus says would be futile and change nothing. As the crowd cheers him on, they suddenly ask "would you die for me?" to which Jesus visibly reacts with concern. Jesus is approached by Simon the Zealot, who suggests that Jesus lead his mob in a war against Rome and gain absolute power ("Simon Zealotes"). Jesus rejects this suggestion, stating that none of his followers understand what true power is, nor do they understand his true message ("Poor Jerusalem").
Pontius Pilate, the governor of Judea, has had a dream in which he meets with a Galilean (Jesus) and that he, Pilate, will receive all of the blame for the man's violent and mournful death ("Pilate's Dream"). Jesus arrives at the Temple in Jerusalem and finds that it has become a haven of sin and debauchery as it is being used for selling everything from weapons to prostitutes and drugs. He is furious and demands that the merchants and money changers leave the temple ("The Temple"). Angry, disconsolate, and tired by his burden, Jesus rests and falls asleep. In a chilling nightmare, he is confronted by lepers, cripples, and beggars, all wanting to be healed. Even though he heals some, their number increases, and he is overwhelmed. Unable to solve everyone's problems, Jesus tells the crowd to heal themselves. He awakes to find Mary Magdalene by his side. She lays him to rest ("Everything's Alright" reprise). While Jesus is asleep, Mary acknowledges that she is unconditionally in love with Jesus, unlike any man she has known before, and it frightens her ("I Don't Know How to Love Him").
Judas gradually becomes more and more envious of Mary; he believes she has usurped him as Jesus' most trusted ally and that he prefers her to his Apostles. Conflicted, Judas seeks out the priests and promises to help them capture Jesus, while belaboring that he is acting with unselfish motives and that Jesus himself would approve if he knew those motives ("Damned for All Time"). Caiaphas demands that Judas reveal the location of Jesus so that the authorities can apprehend him. In exchange for the information, Judas is offered money as a "fee" so that he can assuage his conscience by using the money charitably. ("Blood Money"). Judas decides that it would be better to turn Jesus in before his popularity leads to the deaths of Jesus and his followers, Judas included. He reveals that on Thursday night, Jesus will be at the Garden of Gethsemane.

Act 2

At what Jesus knows will be the Last Supper, he pours wine and passes bread for his apostles. He's very aware of the ordeal he faces and a little stung when the others don't pay much attention to him. "For all you care this wine could be my blood / For all you care this bread could be my body," he remarks ("The Last Supper"), in a revision of the Christian doctrine of the Eucharist. He asks them to remember him when they eat and drink. Jesus predicts that Peter will deny him three times "in just a few hours" and that one of them will betray him. Judas admits he is the one, believing that Jesus already knows ("cut the dramatics, you know very well who"), and angrily accuses Jesus of acting recklessly and egotistically. Following an admission that he doesn't understand Jesus' decisions, he leaves Jesus and the apostles to bring the Roman soldiers. The remaining eleven apostles fall asleep, and Jesus goes to the Garden of Gethsemane to pray. He admits his doubts, fears and anger to God, that he is tired and has done all he can; he asks powerfully if any of it had meaning and implores God not let him suffer the horrible death planned for him. He feels disillusioned with his quest as the Messiah, does not understand what it has achieved, and wishes to give up. Receiving no answer, Jesus realizes that he cannot defy God's will, and surrenders to God; his prayer ends with a request that God take him immediately "before I change my mind" ("Gethsemane (I Only Want to Say)").
Judas arrives with Roman soldiers and identifies Jesus by kissing him on the cheek. Jesus is arrested, and his apostles attempt to fight the soldiers. Jesus tells them to let the soldiers take him to Caiaphas. On the way, a mob (acting like - and sometimes represented as - modern-day news reporters) asks Jesus what he plans to do, but Jesus declines to comment. When Jesus is brought to trial before the Sanhedrin, Caiaphas asks if he is the son of God. Jesus responds: "That's what you say, you say that I am." This answer is affirmative according to Jewish custom, and that provides enough justification for the high priests to send Jesus to Pontius Pilate ("The Arrest"). Meanwhile, Jesus' apostle Peter is confronted by an old man, a soldier and a maid, and Peter denies to each that he knows Jesus. Mary asks Peter why he denied Jesus, and Peter responds that he had to do it in order to save himself. Mary wonders how Jesus knew that Peter would deny him three times ("Peter's Denial").
Pilate asks Jesus if he is the son of God. Jesus gives the same answer that he gave Caiaphas: "that's what you say." Since Jesus is from Galilee, Pilate says that he is not under his jurisdiction and sends him to King Herod ("Pilate and Christ"). As Jesus is dragged away, the chorus asks where Jesus' power has gone ("Hosanna"). In a mocking ragtime number, the decadent and flamboyant King Herod asks Jesus to prove his divinity by performing miracles, offering to free him if he complies; but Jesus ignores him. Herod decides that Jesus is just another phony messiah and angrily sends him back to Pilate ("Herod's Song (Try It and See)"). The apostles and Mary Magdalene remember when they first began following Jesus, and wish that they could return to a time of peace ("Could We Start Again, Please?") Feeling extreme guilt for Jesus' harsh treatment by the authorities, and panicking that he will be seen as responsible, Judas expresses regret to the priests, fearing he will forever be remembered as a traitor. Caiaphas and Annas say that what he has done will save everyone and that he should not feel remorse for his actions before throwing him out of their temple. Left alone, recognition dawns that memories of this could haunt the rest of his life, that God chose him to be the one to betray Jesus, and that he has been used as a pawn for the "foul bloody crime". He suffers a mental breakdown during the epiphany, cursing God for his manipulative ways, and in a final attempt to detach himself from his destiny, he commits suicide by hanging himself from a tree ("Judas' Death").
At Jesus' trial, Pilate asks the crowd if they would crucify Jesus, their king, and they declare: "We have no king but Caesar!" Pilate remembers the dream he had about the crowd and the unjust execution of Jesus ("Pilate's Dream" instrumental). Pilate tells the crowd that, while Jesus should be imprisoned, he does not deserve to die. Pilate demands that the crowd give him a reason to condemn Jesus, and the crowd breaks into a pep rally-style cheer about how Jesus is a blasphemer and has defied Rome. After revealing Jesus as nothing more than a pathetic human being ('Behold the man!"), Pilate calls the crowd hypocrites, as he knows they hate Roman rule. He attempts to satisfy their bloodlust by having Jesus whipped, counting thirty-nine bloody strokes. Pilate, clearly disturbed by the whole ordeal, pleads with Jesus to defend himself; but Jesus says weakly that everything has been determined (by God), and Pilate cannot change it. The crowd still screams for Jesus to be crucified, and Pilate recalls his duty to keep the peace. He reluctantly agrees to crucify Jesus to keep the crowd from getting violent ("Trial Before Pilate (Including the Thirty-Nine Lashes)"). Pilate then washes his hands of Jesus' death: "I wash my hands of your demolition/Die if you want to, you innocent puppet".
As Jesus prepares to be crucified, he is mocked by a vision of Judas. Judas questions why Jesus chose to arrive in the manner and time that he did, and if what happened to him was really part of a divine plan, but Jesus does not say ("Superstar"). As Jesus is nailed to the cross, some productions opt to show Judas suffering a stigmata-like effect, indicating that he is paying for his sin. After reciting his final words and condemning his spirit for God, Jesus slowly dies on the cross, his fate coming full circle ("The Crucifixion"). The final instrumental number shows the Apostles, Mary and Judas mourning the death of their fallen savior, reflecting on the impact he's had on their lives ("John Nineteen: Forty-One").