With the words "Once Upon a Time", the Narrator introduces four characters who each have a wish: Cinderella, who wishes to attend the King's festival; Jack, a simple young man who wishes that his cow, Milky-White, would give milk; and the Baker and his Wife, who wish they could have a child. While Little Red Ridinghood buys bread from the Baker to take to her grandmother's house, Jack's weary mother nags him into selling the cow, and Cinderella's stepmother and sisters tease her about wanting to attend the King's festival.
The Baker's neighbor, an ugly old witch, reveals the source of the couple's infertility is a curse she placed on the Baker's line, after catching the Baker's father in her garden stealing "magic" beans. In addition to the curse, the Witch took the Baker's father's newborn child, Rapunzel (Witch's Entrance). The curse will be lifted if the Baker and his Wife can find the four ingredients that the Witch needs for a certain potion — "the cow as white as milk, the cape as red as blood, the hair as yellow as corn, and the slipper as pure as gold", all before the chime of Midnight in three days' time. All begin their journeys into the woods — Jack goes to the market to sell his beloved pet Milky White, Cinderella's family goes to the Festival, Cinderella to her mother's grave to ask for guidance, Little Red to her Grandmother's house, and the Baker, refusing his wife's help, to find the ingredients (Prologue).
Cinderella visits her mother's grave and receives a beautiful gown and golden slippers from her mother's spirit (Cinderella at the Grave). Jack encounters a Mysterious Man, who mocks him for trying to sell his cow for more than a "sack of beans" and then vanishes. Little Red Ridinghood meets a hungry wolf who convinces her to take a detour on her way to Granny's, and then dashes off to consume the old woman (Hello, Little Girl). The Baker sees Little Red in the woods and when the Witch appears, screaming at him to get the red cape, she frightens him so much he forgets the ingredients he needs. Luckily his Wife, who followed him into the forest, reminds him. They are squabbling over her presence when they come across Jack with Milky-White. Not having the money necessary to buy the cow, they convince Jack that the beans the baker has found in his father's old hunting jacket are "magic", and buy the cow for five of them. Jack bids a tearful goodbye to his cow (I Guess This Is Goodbye), and the Baker orders his Wife to return to the village with the cow. He has qualms about being so dishonest, but his wife reasons that the end justifies the beans (Maybe They're Magic)
Meanwhile, it is revealed that the Witch has raised Rapunzel as her own daughter, keeping her locked away from the world in a tall tower in the middle of the woods, accessible only by climbing Rapunzel's long, golden hair (Our Little World). However, a handsome Prince spies the beautiful Rapunzel, and resolves to climb the tower himself. In another part of the wood, the Baker has tracked down Little Red Ridinghood. Following the Witch's advice, he attempts to simply steal the red cape, but her ensuing temper tantrum guilts him into returning it. When the girl arrives at her grandmother's house, she is swallowed by the Wolf. The Baker in pursuit of the cape, slays the Wolf, pulling Little Red and her grandmother from the beast's innards. Little Red rewards him with the red cape, boasting of her new experiences (I Know Things Now). Meanwhile, Jack's mother angrily tosses the beans aside and sends her son to bed without supper. As Cinderella flees the festival, pursued by another handsome prince and his steward, the Wife helps her hide and quizzes Cinderella about the ball. Cinderella explains that it was a nice ball with "A Very Nice Prince", but seems fairly ambivalent about the experience. As a giant beanstalk begins to sprout from the ground next to Jack's cottage, the Wife spots Cinderella's pure gold slippers. She tries to chase after Cinderella, inadvertently allowing Milky-White to run off, leaving the Wife without the slippers and the cow. The characters each state morals and credos as the First Midnight chimes (First Midnight) and they continue their journeys through the woods.
The next morning, Jack describes his thrilling adventure after he returns from climbing the beanstalk (Giants in the Sky). He gives the Baker five gold pieces he stole from the giants to buy back his cow, and when the Baker hesitates, Jack climbs back up the beanstalk to find more. The Mysterious Man emerges and taunts the Baker, stealing the money. The Baker's wife confesses she has lost the cow, and she and the Baker split up to look for it. Cinderella's and Rapunzel's Princes, who are brothers, meet and compare the misery of their new-found and unobtainable loves (Agony). The Baker's wife, who is eavesdropping, takes note when Rapunzel's prince mentions that he is in love with a girl in a tower with hair as "yellow as corn". The Baker's Wife fools Rapunzel into letting down her hair and pulls out a piece of it. Meanwhile, The Mysterious Man gives Milky-White back to the Baker.
The Wife and Cinderella meet again, and the Wife makes a desperate grab for her shoes, almost succeeding before Cinderella flees. The Baker and his wife reunite, now with three of the four items. The Baker admits that they've had to work together to fulfill the quest (It Takes Two). Jack arrives with a hen that lays golden eggs and attempts to buy Milky-White back, but the cow suddenly keels over dead as midnight chimes. Again, the characters exchange morals (Second Midnight). The Witch discovers that the Prince has been visiting Rapunzel and begs Rapunzel to stay with her (Stay with Me). When Rapunzel refuses, the Witch angrily cuts off Rapunzel's hair and banishes her to a desert. The Mysterious Man gives the Baker the money to buy another cow, and Jack, goaded by Little Red Ridinghood, who is now sporting a wolf skin cape and a knife for protection, returns once again to the Giant's home to steal a magic harp.
Cinderella's Prince spreads pitch on the stairs of the castle to try to capture her. She escapes, but leaves one of her slippers (On the Steps of the Palace) as a clue to her identity. The Baker's Wife tries to trade her own shoes and the last bean for Cinderella's slipper; Cinderella throws the bean aside, but trades shoes with the Baker's wife and flees. The Baker arrives with another cow; they now have all four items. A great crash is heard and Jack's mother reports that a Giant has fallen from the beanstalk and is dead in her backyard. The Witch discovers that the new cow is not pure white — it is covered with flour. However, the Witch revives Milky-White, and the Baker and his Wife feed the items to her. Jack milks her, but no milk comes. The Baker's Wife reveals that the hair is Rapunzel's, and the Witch furiously explains that the magic will not work, because the Witch has already touched Rapunzel's hair. The Mysterious Man tells the Baker to feed the hair-like corn silk to the cow. Now Milky-White gives milk, which is the potion. The Witch reveals that the Mysterious Man is the Baker's father. The Witch drinks the potion and suddenly the Mysterious Man falls dead, his reparation complete. The curse is broken, and the old ugly Witch is again young and beautiful.
Cinderella's Prince searches for the girl whose foot fits the slipper; the stepsisters try but can only get it on by cutting off parts of their feet, then Cinderella appears, her foot fits the slipper, and she becomes the Prince's bride. Rapunzel has borne twins in the desert where her Prince finds her. The Witch attempts to curse the couple, only to find that her powers have been lost. At Cinderella's wedding to the Prince, the stepsisters are blinded by birds as they try to win Cinderella's favor. Everyone but the Witch and the stepsisters congratulate themselves on being able to live happily "Ever After", though they fail to notice another beanstalk growing sky-high in the background.
Later all the characters seem happy but are, ironically, still wishing: The Baker and his Wife have their precious baby boy, but wish for more room; Jack and his mother are rich and well-fed, but Jack misses his kingdom in the sky; and Cinderella is living with her Prince Charming in the Palace, but is getting bored (So Happy).
Suddenly, everyone is knocked over by a loud crash, and enormous footprints have destroyed the Witch's garden, sparing only a few beans. The Baker and his Wife decide that they must tell the Royal Family but first they safely escort Little Red Ridinghood to her grandmother's house after her mother was killed by the Giant. Jack decides that he must slay the Giant and Cinderella learns from her bird friends that her mother's grave was disturbed and decides to investigate (Into the Woods (Reprise)).
While everyone else is drawn back into the woods, Rapunzel has fled there in a hysterical fit, her treatment at the hands of the Witch having driven her into madness. Her Prince has followed her, but when he encounters his brother they each confess they have another reason for their presence in the woods: they have grown bored and frustrated with their marriages and now lust after two beautiful women asleep in the woods - Snow White and Sleeping Beauty (Agony (Reprise)).
The Baker, his Wife and Little Red Ridinghood get lost in the woods and find the Witch, who brings news that their houses have been destroyed, and the Royal Family and the Steward, who reveal that the castle was set upon by the Giant. The Giant then appears. This Giant is a woman, the widow of the Giant that Jack killed by chopping down the beanstalk. Her booming voice proclaims that she wants Jack's blood in revenge. To satisfy the Giantess, everyone offers her the narrator as a sacrifice, until they realize how lost they would be without him. Nevertheless, the Witch throws him into the Giantess's arms and he is killed. Jack's mother finds the group and aggressively defends her son, angering the Giantess, and the Steward clubs Jack's mother to quiet her, inadvertently killing her. The Giantess leaves to search for Jack, and Rapunzel runs underneath the Giantess and is trampled, to the horror of the Witch and her Prince (Witch's Lament).
The Witch declares she will find Jack and sacrifice him to the Giant, and the Baker and his Wife decide they must find him first and split up to search. The Baker's Wife meets Cinderella's Prince, and he easily seduces the Wife (Any Moment). Meanwhile, the Baker discovers Cinderella at her mother's destroyed grave and convinces her to join their group for safety. The Prince, satisfied, leaves the Baker's Wife with a few platitudes, and she realizes her error and decides to return to her happy life with the Baker and their son (Moments in the Woods) just moments before being accidentally crushed by the angry Giantess.
The Baker, Little Red Ridinghood, and Cinderella await the return of the Baker's Wife when The Witch drags in Jack. The Baker, grief-stricken when he learns of his wife's death, unwittingly agrees to give Jack to the Giantess, causing an argument. The characters first blame each other for their predicament, until finally they all decide to blame the Witch for growing the beans in the first place (Your Fault). Disgusted, the Witch curses them, throws away the rest of her magic beans, reactivating her mother's curse and making her vanish (Last Midnight).
The grieving Baker flees but is visited by his father's spirit, who convinces him to face his responsibilities (No More). The Baker returns and helps plan to kill the Giantess, using Cinderella's bird friends to peck out the Giant's eyes at an area smeared with pitch, where Jack and the Baker can finally deliver a fatal blow. Cinderella stays behind to protect the Baker's child, when her Prince appears and explains his reasons for seducing another woman. Feeling both hurt and angry, she demands that he leave her. Little Red returns with the news that her grandmother has been killed by the Giantess. The Baker tells Jack that his mother is dead. Jack vows to kill the steward in revenge, until the Baker convinces him that killing the steward will not benefit anyone. Cinderella comforts Little Red and tries to answer her qualms that killing the giant makes them no better than she is, while the Baker explains to Jack his inability to say what is really morally correct (No One Is Alone).
The four remaining characters slay the Giant, and each of the previously deceased characters (save the Princes, the Steward, and the Royal Family) returns to describe the lesson they learned. The survivors plan to rebuild their lives together, and The Baker's Wife returns (in the form of a spirit) to give her husband one final lesson: Tell their child the story of the Woods; actions have consequences — even for future generations. The Baker begins to tell the story as the Witch appears, with the final moral: Be careful what you pass on to your children (Children Will Listen). All join in on a last reprise of the title song, surmising that we all must venture Into the Woods, but never to forget the past (Finale). Cinderella ends with: "I wish..."