The play begins with a Leading Player of a troupe and the accompanying actors in various costume pieces of several different time periods, establishing the play's intentionally anachronistic, defamiliarized, unconventional feel. Channeling the style of Bertolt Brecht, Hirson breaks the fourth wall, and the Leading Player and his troupe speak directly to the audience. They invite members of the crowd to join them in a story about a boy prince searching for fulfillment ("Magic to Do"). They reveal that the boy who is to play the title character is a new actor. Pippin tells the scholars of his dreams to find where he belongs ("Corner of the Sky"), and they happily applaud Pippin on his ambitious quest for an extraordinary life. Pippin then returns home to the castle and estate of Charlemagne (King Charles), his father. Charles and Pippin don't get a chance to communicate often, as they are interrupted by nobles, soldiers, and courtiers vying for Charles' attention ("Welcome Home"), and Charles is clearly uncomfortable speaking with his educated son or expressing any loving emotions. Pippin also meets up with his stepmother Fastrada, and her dim-witted son Lewis. Charles and Lewis are planning on going into battle against the Visigoths soon, and Pippin begs Charles to take him along so as to prove himself. Charles reluctantly agrees and proceeds to explain a battle plan to his men ("War is a Science").
Once in battle, the Leading Player re-enters to lead the troupe in a mock battle using top hats, canes, and fancy jazz as to glorify warfare and violence ("Glory"). Fosse's famous "Manson Trio" is performed by the Leading Player and his two lead dancers in the middle of this number. This charade of war does not appeal to Pippin, and the boy flees into the countryside. The Leading Player tells the audience of Pippin's travel through the country, until he stops at his exiled grandmother's estate ("Simple Joys"). There, Berthe (his grandmother, and Charles's mother, exiled by Fastrada) tells Pippin not to be so serious and to live a little ("No Time At All"). She sings, "Oh, it's time to start livin'. Time to take a little from this world we're given. Time to take time, cause spring will turn to fall in just no time at all." Pippin takes this advice and decides to search for something a bit more lighthearted ("With You"). While he initially enjoys these meaningless sexual encounters, he soon discovers that relationships without love leave you "empty and unfulfilled."
The Leading Player then tells Pippin that perhaps he should fight tyranny, and uses Charles as a perfect example of an unenlightened tyrant to fight. Pippin plans a revolution, and Fastrada is delighted to hear that perhaps Charles and Pippin will both perish so that her beloved Lewis can become king. Fastrada arranges the murder of Charles, and Pippin falls victim to her plot ("Spread a Little Sunshine"). While Charles is praying at Arles, Pippin murders him, and becomes the new king ("Morning Glow"). However, after petitions from the masses, Pippin realizes that neither he nor his father could change society and had to act as tyrants. He begs the Leading Player to bring his slain father back to life, and the Leading Player does so. At this point in the currently licensed production, the Leading Player then introduces Pippin to The Finale.
Pippin is left without direction until the Leading Player inspires him ("On the Right Track"). After experimenting with art and religion, he falls into monumental despair and collapses on the floor. Catherine finds him on the street, and is attracted by the arch of his foot ("And There He Was") and when Pippin comes to, she introduces herself to Pippin ("Kind of Woman"), a widow, with a small boy, Theo. From the start, it is clear that the Leading Player is concerned with Catherine's actual attraction to Pippin—after all, she is but a player playing a part in his yet-to-be-unfolded plan. At first, Pippin thinks himself above such boring manorial duties as sweeping, repairs, and milking cows ("Extraordinary"), but eventually he comforts Theo on the sickness and eventual death of his pet ("Prayer for a Duck") and warms up to the lovely Catherine ("Love Song"). However, as time goes by, Pippin feels that he must leave the estate to continue searching for his purpose. Catherine is heartbroken, and reflects on him (much to the Leading Player's anger and surprise) ("I Guess I'll Miss the Man").
All alone on a stage, Pippin is surrounded by the Leading Player and the various troupe members. They all suggest that Pippin complete the most perfect act ever: the Finale. They tell Pippin to jump into a box of fire, light himself up, and "become one with the flame." Pippin is reluctant at first, but slowly loses resistance ("Finale"). He is stopped by his natural misgivings and also by one actress from the troupe—the woman playing Catherine. Catherine and her son Theo stand by Pippin and defy the script, the Leading Player, and Fastrada. Pippin comes to the realization that the widow's home was the only place where he was truly happy ("Magic Shows and Miracles") "...I never came close my love". Having experimented with every possible path to fulfillment, he feels humbled, and realizes that maybe the most fulfilling road of all is a modest, ordinary life. He comes to the conclusion that, while "settling down" may at times be mundane and boring, "if [he's] never tied to anything, [he'll] never be free." After removing the sets, lighting, makeup, and costumes from the stage (to no success at dissuading Pippin), The Leading Player becomes furious and calls off the show, telling the rest of the troupe and the orchestra to pack up and leave Pippin, Catherine, and her son alone on an empty, dark and silent stage: "You try singing without music, sweetheart!" Pippin realizes that he has given up his extraordinary purpose for the simplest and most ordinary life of all, and he is finally a happy man. Well, perhaps. When Catherine asks him if he feels like a compromiser or a coward, he says no. But he does feel "trapped," and that, so he says, "isn't too bad for the end of a musical comedy."
Alternate ending
The currently licensed edition of Pippin has a slightly different ending. After the troupe throws their gloves at Pippin, and he avers his contentment with a simple life with Catherine, Theo remains on stage, picks up a glove and sings a verse of "Corner of the Sky", after which the Leading Player and the troupe return onto the stage. The Leading Player reaches a hand out to Theo. Pippin and Catherine return, watching in fear, unable to do anything. The light on Theo becomes brighter, and presumably, the cycle continues. Blackout. Current productions vary between the two possible endings, though Schwartz himself has expressed his preference for the newer ending.