The show begins with the Voice of God declaring his supremacy: "My name is Known: God and King. I am most in majesty, in whom no beginning may be and no end." The company enters and takes the role of various philosophers throughout the ages (often this section of the play is excluded): Socrates; Thomas Aquinas; Leonardo da Vinci; Edward Gibbon; Jean-Paul Sartre; Martin Luther; Friedrich Nietzsche; and Buckminster Fuller. (In the revival, Gibbon, Luther, Nietzsche, and Fuller were replaced by Galileo Galilei, Jonathan Edwards, Marianne Williamson, and L. Ron Hubbard, respectively.) They sing fragments of their respective philosophies — first as solos and then in cacophonous counterpoint — in "Tower of Babble (Prologue)". In some productions, "Tower of Babble" is replaced by "Beautiful City", which Jesus sings to open the show. In still other productions, the company cuts Tower of Babble and Beautiful City, opting to begin with "Prepare Ye (The Way of the Lord)".
In response to the philosophers, John the Baptist blows three notes on the shofar to call the community to order. He then beckons them to "Prepare Ye (The Way of the Lord)", and baptizes the company (this can be done in various ways, aiming to be comical). Jesus comes, also to be baptized. John responds by, instead, asking to be baptized by Jesus. Jesus explains that it is not his place to baptize; that he has come to "Save the People".
In his first parable, Jesus explains to the company that he has come "not to abolish the law and the prophets, but to complete". In the original production, the company donned clown makeup at this point. Subsequent productions may instead use some object—a pin, a scarf, a badge, or a flower, for example—to denote that the company has become followers of Jesus. Jesus explains to the company that those who adhere to the law of God will earn the highest place in the Kingdom of God. He tells them the story of the widow and the Judge: God is a just jurist who will support those who cry out to him.
The company begins to understand Jesus and his teachings, and they take it upon themselves to tell the story of the Pharisees and the tax gatherer praying in the temple: "Every man who humbles himself shall be exalted!"
As Jesus teaches of the law regarding the offering of gifts at the altar, the company makes offerings—themselves. They are taught that to approach the altar of God, they must be pure of heart and soul.
Then, they act out the story of a master and a servant who owes him a debt. The servant asks his master for pity in repaying the debt, and the master absolves it. The servant then turns to a fellow servant who "owed him a few dollars" and demands that it be paid in full. The master, hearing this, then condemns the servant to prison. Jesus explains the moral: "Forgive your brothers from your heart." The member of the company telling the parable sings "Day by Day", and the company joins in. After the song, Jesus teaches that if one part of you offends God, it is better to lose it than to have the whole of the body thrown into hell.
The company then plays charades (in the current production, with members from the audience) to finish several statements posed by Jesus, including "If a man sues you for your shirt..." and "If a man asks you to go one mile with him....".
Then, a cast member comes forward after charades saying: "You wanna see a show?" The company performs the Parable of the Good Samaritan in the form of a play-within-a-play. Jesus explains the need to "love your enemies", and "not make a show of religion before men". He goes on to say: "God will reward a good deed done in secret." ("Shhh! It's a secret!")
The parable of Lazarus and the rich man is next tackled by the company, who are quickly learning how to work together. On earth, the rich man feasts, and Lazarus begs and is ignored. Upon dying, Lazarus is rewarded with Heaven, while the rich man is in Hell. We are told to "Learn Your Lessons Well", or be faced with eternal damnation. When the rich man asks Abraham if he would send Lazarus back from the dead to warn his brothers of their impending doom, Abraham tells him no: "If they do not listen to Moses and the Prophets, they will not be convinced even if someone should rise from the dead."
Jesus teaches that no man can serve two masters—God and money. A member of the company tells a story of a man who spent a lifetime acquiring the good things in life, then dies before he has the time to enjoy them. She sings "Bless the Lord," then Jesus tells them not to worry about tomorrow: "Tomorrow will take care of itself. Today has problems of its own."
In an antiphonic chorus, the company recites the Beatitudes. Judas, however, directs the final beatitude regarding persecution at Jesus, and Jesus quickly changes the subject. ("Did I ever tell you that I used to read feet?") However, with this Jesus persuades the company that it is "All for the Best"; heaven contains the ultimate reward. Judas sings a verse, and the two do a soft shoe and a vaudevillian joke. The company, and chorus if used, join in the final verse (sung in counterpoint) to bring the song to conclusion.
This is followed by the parable of the Sower of the Seeds, which Jesus tells them represent the Word of God. "All Good Gifts" is sung to further illustrate the point.
The action to this point, while amusing and entertaining, has been to do one thing—create from this rag-tag company a community of love and caring. At this point in the musical, they have formed this community and they now march as soldiers in the military, signifying their ability to think as one unit. With Jesus as the drill sergeant, they segue into the famous Parable of the Prodigal Son. They sing "Light of the World" about Christ's Light and how it should shine in each of us. Jesus thanks the audience for coming, and announces a ten-minute intermission. In the original production, the cast joined the audience for wine and bread. In the current Broadway production, wine is offered to the audience on-stage.
 Act Two
The second act opens with one or more cast members singing "Learn Your Lessons Well", to call the audience back into the hall. Another member of the community sings "Turn Back, O Man", in which she implores mankind to give up its temporal pursuits and to turn to God.
Jesus says: "This is the beginning."
At this point, several members of the community begin to question Jesus's authority, and he responds with yet another parable. He is asked, "What is the greatest commandment?" and responds, "You shall love the Lord your God with all your heart and all your soul... And the second is like it: 'You shall love your neighbor as yourself.'" The Pharisees continue to question him, and he laments "Alas for You", and calls them hypocrites. Members of the community gather and join in his song, and throw garbage at the Pharisees.
Jesus predicts that he will not be seen for quite a while, while standing at the "Wailing Wall", and predicts great wars and famines. He reminds us of the time of Noah, and teaches that faith can calm the storm. The community is told: "Keep awake, then. For the Son of Man will come at a time when you least expect it."
One woman is cast out as an adulteress. Jesus says: "Let the one of you who is faultless cast the first stone." Her accusers then bow their heads and walk away. Jesus walks over to her and asks: "Woman...where are they now? Has no one condemned you?" The woman answers: "No one, sir." He tells her: "Then nor shall I. You may go, but do not sin again." As she watches Jesus walk from her,she entreats him to remain "By My Side". During this song, we see Judas foretell his upcoming betrayal of Jesus.
In one of the lighter moments in the second act, Jesus tells how he will separate men as a shepherd separates his flock into sheep and goats. The sheep will enter heaven while the goats must suffer eternal damnation. "We Beseech Thee" cry the goats, begging for mercy.
After the song, the community reminds each other to take things "Day By Day", as they remove their clown makeup (or other accoutrement). They assemble for the Last Supper, and Jesus tells them that one of them will betray him. Each member of the community asks, "Is it I?" ending with Judas: "Rabbi...can you mean me?" Jesus tells him to do quickly what he must do, and Judas runs off. Jesus breaks the bread and shares the wine and tells his followers that they will dine together in the Kingdom of Heaven. He asks that they wait for him as he goes into the Garden of Gethsemane to pray. The band sings "On the Willows", which is about what has been sacrificed. In the song, Jesus says goodbye to the company members.
In the garden, Jesus implores God that if there is another way, to let the burden be lifted from his shoulders. He is tempted by Satan, but orders him away. Jesus returns to his followers to find them all asleep.
Judas returns and kisses Jesus on the cheek, to bring him to be crucified. The community starts to attack Judas, while Jesus reminds them: "He who lives by the sword, will die by the sword... This has all happened to fulfill what the Prophets have written."
The "Finale" begins, loud and in B Major, with Jesus being put upon an electric fence, representative of the cross described in the gospel of Matthew. Jesus wails, "Oh, God, I'm dying," and the community answers: "Oh, God, You're dying." Jesus dies and the music comes to a rest. One woman sings "Long Live God", joined on each phrase by another female voice. The men join in with "Prepare Ye the Way of the Lord" in counterpoint, as they remove Jesus from the fence and carry him out (either offstage or through the aisles of the auditorium). There is controversy over the fact that there is no obvious resurrection of Jesus present in the show, although some see either the singing of "Prepare Ye" in the finale or else the curtain call (where all including Jesus return to the stage) as representative of the resurrection. Some productions have placed the song "Beautiful City" after the finale to show the resurrection.