Our story begins with a council of angels who look down on a polluted war-scorched Earth with sadness and sympathy ("Where Have We Gone?") The angels are tasked with electing a prophet of yesteryear to restore the Earth to its former glory. God himself intervenes (through his nerdy young intern) to declare that Jesus Christ will be given the task. Meanwhile. Jesus is partying in a heavenly Las Vegas style nightclub drinking sloppy with history's most famous dead people ("I'm Doing Fine"). Before returning to Earth, Jesus meets with the council who introduce him to his bandmates and companions for the trip: the great warlord Genghis Khan on the drums, the ancient Greek philosopher Socrates on the bass, and the diarist Anne Frank on guitar.
As Jesus and his band land on Earth. They immediately encounter an army of brutish Slavers torturing a local peasant. Deciding to rescue him, the band attempts to distract the roguish marauders by performing one of Jesus· hits ("So Says the Man"). When the song comes to an end, the Slavers are blown away and become fanatical Jesus fans. Convincing them to spread the good word, Jesus sends them out into the desert. As a token of gratitude for saving his life, the peasant (named Bluebird Givvens) leads the group back to his town: Jen's Oasis. Once there, Jesus finds a thriving community who has renounced religion and instead follows the idealistic atheist and performer Jen Compton. Sneaking into one of her rallies, the band watches Jen perform a flamboyant musical theatre number ("People"). Seeing an opportunity to steal her spotlight, Jesus interrupts Jen's rally and uses his magical powers to gradually turn the crowd against her. Afterwards, he announces his grand plan: in 7 days he will be crucified; then resurrected in a miraculous stadium rock show ("Resurrection").
Now worshipped by the people of Jen's Oasis, Jesus makes preparations for his ambitious crucifixion show. However, doubt begins to creep into his mind when some of his past actions catch up to him. Pathos, Bluebird's sickly son, was healed by Jesus. But now it appears that there were side-effects to this opportunistic attempt to win favour with the people. Pathos has gone blind. Furthermore, Jen's Oasis has descended into lawlessness, leaving the Giwen's Family, homeless. Struggling with the mounting pressure of the show and guilt over what he's caused. Jesus decides to cancel at the last minute and run off to the desert to find inspiration ("Who I Am"). Joined by his bandmates and entourage, Jesus throws a bacchanalian party turning the group's only casks of water into wine ("Oh What A Fool"). The next morning, he awakens to discover an abandoned campsite with only his bandmates waiting for him. It appears his miracle wine made everyone sick, showing a defect in his powers and causing his now jaded entourage to flee back to Jen's Oasis.
Deciding to continue their journey, Jesus and the band soon encounter a pair of punk anarchist highwaymen who rob them of nearly all their possessions. Now stranded in the desert with no food or money, the group makes their way to a small outpost where they decide to perform for money and food. However, Jesus is in low spirits and their show doesn't go over well with the crowd of nomadic peasants. They are soon upstaged by a young Jen Impersonator who performs one of her idol's hits to a receptive crowd ("Forgiveness"). Feeling deeply insecure and overshadowed by Jen, Jesus resolves to write a new song and win back the audience. But when he plays the rushed composition to his bandmates. they are less than enthusiastic. Offended by what he perceives as their lack of support, an argument breaks out and the band members soon quit.
Jesus, now alone, returns the borrowed guitar he was using to an Old Man who lives at the outpost. Recognizing Jesus· lack of inspiration, he encourages him to travel to the Rock 'n· Roll History Museum, a broken down old shrine where it is said the mystical forces of old still reside. Intrigued. Jesus travels alone through the desert in search of the fabled museum ("Follow the Lines") Filthy and exhausted. He at last discovers the museum and enters ("Still Believin'"). There, he encounters the spirits of many great prophets and deities of old: Moses, Krishna, Buddha, Zeus, and Amertasu. They teach him that everyone can be a vessel for God, but only if they do it with humility and love ("Holy Moses"). The moment of enlightenment is interrupted by a roar of motorcycle engines as the Slavers from earlier burst into the museum. Overhearing their conversation, Jesus learns that they are on their way to Jen's Oasis to see a new crucifixion show ... with Jen as the replacement sacrifice! As he is about to sneak away, one of the slavers notices Jesus and.not recognizing him in his filthy sun ravaged state, takes him captive as a slave. Jesus and Jen now both prisoners lament over their hopeless situations ("Pray for Me").
In a glimmer of hope, Jesus is reunited with his band when they are also picked up by the Slavers. Taking the opportunity to apologize and share what he learned on his journey alone, the band soon makes up and decides to rescue Jen. Meanwhile, the Slavers path is blocked by a pack of mutated mules. who stand stubbornly in the way of their vehicles. Jesus and his band are soon ordered to move the animals out of the way giving them an opportunity to escape. Calling on God to provide some divine intervention, the band's instruments are miraculously returned to them and they sonically overwhelm the Slavers causing the army to scatter ("Resurrect and Rebuild"). Now free, the group returns to Jen's Oasis on the backs of the mutated mules.
At the town's entrance, the group encounters a burning lawless husk of what once was distraught. Jesus quickly devises a complex plan to rescue Jen and save the town. Anne and Socrates are tasked with breaking into the backstage area of the venue where the crucifixion is set to take place that night and stalling the crowd. Meanwhile, Jesus and Genghis infiltrate the prison where Jen is being held and break her out. Though at first reluctant to go with them, Jesus explains that he has changed his ways. He now realizes that Jen is the true saviour the people need and believes that she should take the stage to set things right. not him ("Since You've Been Around"). Recognizing his transformation, Jen agrees to perform. Just as Anne and Socrates are about to lose control of the unruly crowd, Jen takes the stage and. to the shock of the audience, announces that she is not going to be crucified. Instead, she calms the crowd speaking about the balance between spirituality and self-determination. arguing that regardless, our first priorities must always be to love each other and realize how everyone is connected ("People Through People"). The crowd cheers. remembering their love for Jen. In an act of appreciation for saving the town, Jen invites Jesus and his band onstage to perform a song together and the crowd goes wild ("Prayin' for the People"). Their mission on Earth complete. Jesus and his bandmates ascend into the sky and board a heavenly spaceship, now on a new quest to spread the good word of Rock n' Roll across the stars!