The show begins with Jesus declaring himself as God and King, in whom there is no beginning and no end. The company takes on the roles of different philosophers – including Socrates, Thomas Aquinas, Martin Luther, Leonardo DaVinci, Frederic Nietzche and Jean Paul Sartre – who debate the existence of the God ("PROLOGUE"). The debate disintegrates into babble, where ideas become only fragments ("TOWER OF BABBLE").
John the Baptist enters and brings order to the proceedings ("PREPARE YE THE WAY OF THE LORD"). John the Baptist baptizes the company, who then quickly exit. When Jesus wishes to be baptized, John kneels and wishes to be baptized by him instead. Jesus brings John back to his feet, and John begins to wash him as Jesus calls his followers to him ("SAVE THE PEOPLE"). The company returns in clown costumes and proudly shows them to each other. From this point forward, John the Baptist becomes Judas. Jesus paints the faces of his followers, marking them as separate from society. He then assures them that he has come not to abolish the law of the prophets, but to complete it. While the company moves like stylized marionettes, Jesus informs them that those who keep to the law of God will earn the highest place in heaven. To illustrate this, he tells the story of the widow and the judge. The story shows that God is a good judge, who will vindicate those who cry out to Him day and night.
He then prompts the company to act out the story of the Pharisee and the tax gatherer praying in the temple, in order to illustrate that every man who humbles himself before God shall be exalted. Jesus preaches the law of offering gifts at the altar before God as the company depicts making offerings. Then, as they all clap in rhythm, they act out the story of a Master and the Servant. The Servant, after asking for the Master's pity and being granted remittance from the debt owed to his Master, refuses to show pity on a fellow Servant who is in debt to him. Learning of the first Servant's reprehensible behavior, the Master condemns him to prison until the debt is paid. Jesus tells the company that the moral of the story is that one must forgive as God forgives.
Following this lesson, one of the company members comes forward to become the first disciple and declare her loyalty to Jesus. She is soon followed by her fellow clowns ("DAY BY DAY"). Jesus proceeds to teach the company more lessons and then leads the company in a game of charades to help them learn yet another lesson. This leads them to do a pantomime of the Good Samaritan story for Jesus, who then tells them to love their enemies and not to make a show of religion. If good deeds are done in secret, the reward will come from God.
The company performs the story of Lazarus and the rich man. Lazarus is a poor man who goes to heaven, and the rich man goes to hell. The rich man begs God to let Lazarus rise from the dead in order to warn his rich brothers of their eventual fate. The message is that one is doomed if one does not follow the law of God ("LEARN YOUR LESSON WELL").
Jesus tells the company that no one can be devoted to two masters, and that no man can serve God and money. One of the company members tells a story of a man who spends his life, accumulating things, and then dies before he can enjoy it. This leads to a member of the company leading the others to bless the Lord, and it is clear by their shared movement that they are beginning to form a community ("OH, BLESS THE LORD MY SOUL"). Jesus bids the company to put away thoughts of material things and anxieties about tomorrow.
The company recites the beatitudes, and Jesus answers them in a call-and-response manner. However, Judas recites the final beatitude about persecution and directs it at Jesus. The company freezes with fear about what events are yet to come. However, Jesus isn't ready for them to know and quickly changes the subject, assuring everyone that they will have a reward in heaven ("ALL FOR THE BEST").
Next, Jesus cautions the company that how they treat others is how they will be treated. This leads to a sequence where the company members behave like school children. One member of the company is singled out and gets stage fright, which causes the other members to laugh at her. Jesus, like a good teacher, helps her start the parable that she is assigned to tell. It is the parable of the sower and the seeds, which represent the word of God ("ALL GOOD GIFTS").
Jesus, acting as a military general, transitions the company into the story of the prodigal son. After that story, Jesus announces that they have reached the end of this particular journey by summing up what they have covered. The company comes together as a true community for the first time and addresses the audience, imploring them to live right and be a beacon for good in the world, as Jesus has just taught them to be ("LIGHT OF THE WORLD").
While one of the company reminds the audience and other disciples what they have learned, the company sets up the stage for Act II ("LEARN YOUR LESSONS WELL – REPRISE"). The second act officially begins when a very sensual company member encourages the audience – and mankind – to give up their foolish ways and turn to God. Jesus joins her entreaty ("TURN BACK, O MAN"). Company members then become Pharisees, who question Jesus' authority. Jesus questions their questions with stories and tells them that the greatest commandment is to love God with all of your heart and to love thy neighbor as thyself. He then scorns the Pharisees and calls them hypocrites ("ALAS FOR YOU"). Some company members join in and throw garbage at the Pharisees.
At the Wailing Wall in Jerusalem, Jesus predicts that he will not be seen again until a future time. He remembers the time of Noah, when the flood swept over the land and drowned mankind. He predicts that, when he comes again, only one man and one woman will be taken with him. The rest will be left outside of the Kingdom of God.
One of the female company members is thrown down onto the stage and called an adulteress. Jesus tells the company that the one who is faultless can throw the first stone at her. When no one condemns her, Jesus assures her that he will not condemn her, either, but that she must not sin again. As he starts to walk away, she asks him to stay with her ("BY MY SIDE").
As Judas betrays Jesus for thirty pieces of silver, Jesus tells of a time when he will sit in glory and divide men into two groups, like a shepherd divides the sheep from the goats. His righteous sheep will enter heaven while the cursed goats will face eternal fire. The goats beg for mercy ("WE BESEECH THEE"). It is time for the company to blend back in with society and pass on the teachings. Jesus removes the face paint that has marked them as a separate company ("DAY BY DAY – REPRISE").
Suddenly, Jesus announces that one of the company will betray him, telling Judas to do what he has to do quickly. Judas runs off. Then, in a recreation of the last supper, Jesus gives the company bread and wine, announcing that it is his body and blood. Although this is the final time they will eat and drink together, they eventually will meet again in the Kingdom of God. Jesus bids farewell to his followers and prays in the garden ("ON THE WILLOWS"). In a moment of uncertainty, he begs for the burden to be lifted from him and is tempted by the devil, but he orders the devil to be gone.
Judas returns and embraces Jesus, who is crucified on the fence upstage while the company climbs the fence and wails. Jesus dies. No one moves. Then, the company removes Jesus from the fence and carries him off ("FINALE").