Act 1
A Narrator introduces four characters: Cinderella, who wishes to attend the King's festival; Jack who wishes his cow, Milky White, would give milk; a Baker; and his Wife, both of whom wish to have a child. Cinderella's step-family mocks her wish and Jack's mother laments that she wishes for wealth. Little Red Ridinghood appears at the bakery wishing for bread and sweets to bring to her grandmother's house. Cinderella's stepmother dumps a pot of lentils into the fireplace for Cinderella to clean up, promising that only then, they will let her go to the festival. To help her, she calls for birds in the skies. Meanwhile, a witch appears at the bakery revealing to the baker and his wife that they are infertile because of a spell she placed on the baker's father many years ago. She explains that his father stole vegetables from the Witch's garden to apease his wife's appetite as she was pregnant. As he was leaving, he stole some beans for himself that he did not realize were magic. When they were taken from the garden, the Witch lost her beauty. In return, she stole their daughter Rapunzel and caused the spell over their family. She explains that the only way to lift the spell is to find four ingredients in the woods: a cow as white as milk, a cape as red as blood, hair as yellow as corn, and a slipper as pure as gold and bring them to her before three days is up. As Cinderella's step-family prepares to leave for the festival, they once again refuse Cinderella's wish to go with them. As he is preparing to leave, the Baker finds six magic beans in his father's old jacket. All begin their journeys into the woods: Jack to sell his beloved cow; Cinderella to seek advice from her mother's grave; Little Red to her grandmother's house; and the Baker, refusing his Wife's help, to find the ingredients ("Prologue: Into The Woods").

When she gets to her mother's grave, Cinderella repeats her wish to attend the festival and the spirit of her mother gifts her with a gown and golden slippers ("Cinderella at the Grave"). A Mysterious Man mocks Jack for valuing his cow more than a "sack of beans". Little Red meets a hungry Wolf who distracts her from her path, hatching a plan to eat both her and her grandmother ("Hello Little Girl"). The Baker, secretly followed by his Wife, meets Jack. Together, they convince Jack that the beans found in the jacket are magic, trade them for the cow and Jack bids Milky White a tearful farewell ("I Guess This Is Goodbye"). The Baker feels guilty about their deceit, but his wife reassures him that it will pay off when they get their child ("Maybe They're Magic").

It is revealed that the Witch has raised Rapunzel in a tall tower, only accessible by climbing Rapunzel's long, golden hair ("Our Little World"); a Prince spies Rapunzel and plans to meet her. When the Baker passes by Little Red's grandmother's house, he finds that the Wolf has eaten them both. In pursuit of her red cape, he stabs the Wolf and rescues Little Red and her grandmother. In return, Little Red gives him her cape, and reflects on her experiences ("I Know Things Now"). When Jack's Mother sees the exchange Jack has made for Milky White, she angrily tosses his beans aside, which grow into an enormous stalk. Cinderella flees the Festival, pursued by another Prince, and the Baker's Wife helps to hide her. When asked about the ball, Cinderella is unimpressed ("A Very Nice Prince"). Spotting Cinderella's gold slippers, the Baker's Wife chases her and loses Milky White as a clock chimes twelve times ("First Midnight").

Jack describes his adventure climbing the beanstalk ("Giants in the Sky") and gives the Baker gold he stole from the giants to buy back his cow. The Baker is hesitant about selling so Jack returns up the beanstalk to find more. The Mysterious Man questions what the Baker cares more about, the money or his child, and takes the money. Cinderella's Prince and Rapunzel's Prince lament over their loves ("Agony") and the Baker's Wife overhears their talk of a girl with golden hair. As she takes hair from Rapunzel, the Baker finds Milky White, aided by the Mysterious Man. The Baker admits they must work together and they hatch a plan to finally seize Cinderella's slipper ("It Takes Two"). Jack arrives with a golden egg as more money for the Baker but Milky White dies as midnight chimes ("Second Midnight"). The Witch discovers the Prince's visits and demands Rapunzel stay sheltered from the world ("Stay with Me"). Rapunzel refuses, and the Witch cuts off her hair, banishing her to a swamp. Jack meets Little Red, now sporting a wolf skin cape and knife. He brags about his adventures in the sky, and mentions a golden harp owned by the Giant. She skeptically goads him into returning to the Giant's home to retrieve it.

Cinderella, torn between staying with her Prince or escaping, leaves him one of her slippers, putting the decision into his hands ("On the Steps of the Palace"), and trades shoes with the Baker's Wife for the last magic bean, though she throws it away in the process. The Baker arrives with another cow and they rejoice over having all four objects, however, the Witch discovers that the Baker has covered a cow in flour to make it appear white. The Witch resurrects Milky White and Jack returns with the harp. A great crash is heard, and Jack's mother reports a dead Giant in her backyard, though no one pays attention. The Witch instructs the Baker to feed the objects to Milky White, though no milk is produced. The Witch learns that the hair is Rapunzel's and will not work because she had touched it. When the Mysterious Man proposes using corn silk instead, Milky White produces the potion and the Witch drinks it, making her young and beautiful once again. She also reveals that the Mysterious Man is the Baker's father, though he dies as soon as she drinks the potion.

Cinderella's Prince seeks the girl who fits the slipper and the desperate stepsisters mutilate their feet, though the Prince sees through it, eventually seeing Cinderella and realizing that she us the one ("Careful My Toe"). Rapunzel is found by her Prince and as the Witch attempts to curse her, she realizes that in exchange for her beauty, she has lost her powers. At Cinderella's wedding, her stepsisters are blinded by birds, and the Baker's Wife, now pregnant, thanks Cinderella for her help. Congratulating themselves on living happily ("Ever After"), the characters fail to notice another beanstalk growing.

Act 2
The Narrator continues, "Once Upon a Time... Later". Everyone still has wishes: The Baker and his Wife face new frustrations with their infant son; newly rich Jack misses the kingdom in the sky; Cinderella is bored with life in the palace ("So Happy"); but all are still relatively content. With a tremendous crash, a Giant's foot destroys the Witch's garden, and damages the Baker's home. The Baker travels to the palace, but his warning is ignored by the Prince's Steward. Returning home, he finds Little Red on her way to Granny's; he and his Wife escort her. Jack decides to slay the Giant and Cinderella investigates her mother's disturbed grave. Everyone returns to the woods, but now "the skies are strange, the winds are strong" ("Into the Woods" Reprise). Rapunzel, driven mad, also flees to the woods. Her Prince follows and meets his brother; they confess their lust for two new women, Snow White and Sleeping Beauty ("Agony" Reprise).

The Baker, his Wife, and Little Red find Cinderella's family and the Steward, who reveal the castle was set upon by the Giant. The Witch brings news that the Giant destroyed the village and the Baker's house. The Giantess – widow of the Giant who Jack killed – appears, seeking revenge. As a sacrifice, the group offer up the Narrator, who is killed. Jack's mother defends her son, angering the Giantess, and the Steward silences Jack's mother, inadvertently killing her. As the Giantess leaves in search of Jack, Rapunzel is trampled ("Witch's Lament"). The Royal Family flee despite the Baker's pleas to stay and fight. The Witch vows to find Jack and give him to the Giantess, and the Baker and his Wife split up to find him first. Cinderella's Prince seduces the Baker's Wife ("Any Moment"). The Baker finds and convinces Cinderella to join their group. The Baker's Wife reflects on her adventure and tryst with the Prince ("Moments in the Woods"), but stumbles into the path of the Giantess and is killed.

The Baker, Little Red, and Cinderella await the return of the Baker's Wife when the Witch arrives with Jack, found weeping over the Baker's Wife's body. The Baker blames Jack and the two, along with Cinderella and Little Red argue and blame each other before all turning on the Witch ("Your Fault"). Chastising their inability to accept the consequences of their own actions, the Witch throws away the rest of her beans, thus regaining her powers so that she can vanish, abandoning the group ("Last Midnight"). Grief-stricken, the Baker flees, but is convinced by his father's spirit to face his responsibilities ("No More"). He returns and lays out a plan to kill the Giantess. Cinderella stays behind with the Baker's child and confronts her Prince over his infidelity; he explains his feelings of unfulfillment and that he was only raised to be charming, but not sincere, and she asks him to leave, which he reluctantly does.

Little Red discovers her grandmother has been killed by the Giantess, as the Baker tells Jack that his mother is dead. Jack vows to kill the Steward but the Baker dissuades and comforts him, while Cinderella comforts Little Red. The Baker and Cinderella explain that choices have consequences, and everyone is connected ("No One Is Alone"). The four together slay the Giantess. The other characters – including the Royal Family, most of whom have starved to death, and the Princes with their new paramours (Sleeping Beauty and Snow White) – return to share one last set of morals. The survivors band together, the Baker, Cinderella, Jack and Little Red decide to live together, and the spirit of the Baker's Wife comforts her mourning husband, encouraging him to tell their child their story. The Baker begins to tell his son the tale, while the Witch and the rest of the characters, dead and alive, offer a final lesson: "Careful the things you say: Children will listen" ("Finale").