Starting with the words "Once Upon a Time," the Narrator introduces four characters who each have a wish: Cinderella, the daughter of a wealthy man who has been reduced by her wicked stepmother and stepsisters into becoming their skivvy, wishes to attend the King's festival; Jack, a simple poor boy, wishes that his cow, Milky White, would give milk; and a Baker and his Wife wish they could have a child.
While Little Red Ridinghood wishes for bread from the Baker to take to her grandmother's house, which they give while she steals a few sweets, Jack's weary mother, who wishes for gold, nags him into selling the cow, and Cinderella's stepmother and stepsisters Florinda and Lucinda tease her about wanting to attend the King's festival.
The Baker's neighbor, an ugly old Witch, reveals that 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 vegetables, including six "magic" beans. In addition to the curse, the Witch took the Baker's father's newborn child Rapunzel. She explains 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 while Cinderella goes to her mother's grave to ask for guidance, Little Red goes to her grandmother's house, and the Baker, refusing his wife's help, goes 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 ("Hello, Little Girl"). The Baker sees Little Red Ridinghood in the woods, and when the Witch appears, screaming at him to get the red cape, he is so frightened that 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 beans 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 chance to have a child justifies their trickery ("Maybe They're Magic”).
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, on this day 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 Little Red Ridinghood 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 Ridinghood and her grandmother from the beast's innards. Little Red Riding hood rewards him with the red cape, reflecting on her new experiences ("I Know Things Now"). Meanwhile, Jack's mother angrily tosses the beans aside, which end up growing into an enormous stalk overnight, 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 ("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 Baker's Wife spots Cinderella's pure gold slippers. She tries to chase after Cinderella but inadvertently allows Milky White to run off, leaving the Baker's Wife without the slippers or 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 and finding a castle of two married giants, whom he robbed unnoticed ("Giants in the Sky"). He gives the Baker five gold pieces he stole from the giants to buy back his cow. 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 Prince and Rapunzel's Prince, who are brothers, meet and compare the misery of their newfound 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 by telling her that she is her prince and pulls out a piece of it. Meanwhile, The Mysterious Man gives Milky White back to the Baker.
The Baker's Wife and Cinderella meet again, and the Baker's 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 will have 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 so she can protect her from the outside world ("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. Jack encounters Little Red Ridinghood, who is now sporting a wolf skin cape and a knife for protection, and tries to impress her by telling her about the kingdom of the Giant. When she refuses to believe him, he is goaded into returning once again to the Giant's home to steal a magic harp.
Cinderella, returning from the last night of the festival, describes how the Prince had spread pitch on the stairs to prevent her from escaping. Caught between wanting to escape and wanting to stay, she eventually resolves to let the Prince decide, leaving him one of her slippers as a clue to her identity ("On the Steps of the Palace"). The Baker's Wife frantically tries to convince her to give up her other shoe, offering her the sixth magic bean in exchange for it. Cinderella throws the bean aside, but trades shoes with the Baker's Wife and flees, while unbeknownst to anyone a second beanstalk starts to grow. The Baker arrives with another cow; they now have all four items. The Prince's Steward grabs the slipper from the Baker's Wife, and they are fighting over it when a great crash is heard and Jack's mother runs in to report that a Giant seeking revenge from Jack for stealing his magic harp has fallen from the first beanstalk when Jack chopped it and is dead in her backyard. The Prince, more concerned with finding Cinderella, waves her off and departs with one of the slippers, giving the other to the Baker and his wife. Jack, to the relief of his mother, returns with the magic harp. The Witch discovers that the new cow is not pure white; it is covered with flour. However, the Witch is able to bring Milky White back to life and instructs the Baker and his Wife to feed the items to her. Jack tries to milk her, but no milk comes. The Baker's Wife admits 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, which is also why she had asked the Baker and his Wife to get the objects for her: she's not allowed to touch any of the objects. 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 Witch is transformed into a beautiful young woman, reversing the effects of the curse of ugliness by which she was punished by her mother, because the Baker's father stole the beans from her, regaining her youth and beauty.
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 ("Careful My Toe"). Cinderella appears, her foot fits the slipper, and she becomes the Prince's bride. Rapunzel has twins in the desert where her Prince finds her. The Witch attempts to curse the couple, only to find that though she gained her youth and beauty, her powers have been lost. At Cinderella's wedding to the Prince, Florinda and Lucinda are blinded by birds as they try to win Cinderella's favor. The Baker's Wife, very pregnant, thanks Cinderella for the slipper. Everyone is at the wedding. 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...
The Narrator introduces the action again: "Once Upon a Time...Later." All the characters seem happy but are still wishing: The Baker and his Wife have their precious baby boy, but wish for more room and bicker over the Baker's unwillingness to hold his child; Jack and his mother are rich and well-fed, but Jack misses his kingdom in the sky; 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 from a Giant have destroyed the Witch's garden, sparing only a few beans. The Baker and his Wife decide that they must tell the Royal Family, and the Baker travels to the palace. His news is ignored by the Prince's Steward, and also by Jack's Mother when he stops at her house to ask for Jack's aid. When he returns home, Little Red Ridinghood arrives on her way to Granny's: her house has been destroyed and her mother is missing. The Baker and his Wife decide to escort her. Meanwhile, 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, dressed in her old clothes. Once again, everyone heads Into the Woods, but this time the mood is somber and the birds have stopped singing ("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 Cinderella's family and the Steward, who reveal that the castle was set upon by the Giant. The Witch arrives as well, bringing news that the Giant has destroyed the village and the Baker's house. Suddenly, thunderous footsteps are heard and the Giant appears. To the shock of all, this Giant is a woman who has come from the second beanstalk and is 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, the group realizes they must give her someone, but are unable to decide on whom until they realize that the Narrator is still commenting on the actions from the sidelines. Everyone offers her the narrator as a sacrifice, but he convinces them how lost they would be without him. Nevertheless, the Witch throws him into the Giantess's arms and he is killed upon being dropped. 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. As the Giantess leaves to search for Jack, Rapunzel runs into her path and is trampled, to the horror of the Witch and her Prince ("Witch's Lament”).
The Royal Family continue on their way, fleeing to a hidden Kingdom despite the Baker's pleas for them to stay and fight the Giant. 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"). However, she has lost her way, stumbles into the path of the Giant, and is consequently killed by a falling tree.
The Baker, Little Red, and Cinderella await the return of the Baker's Wife when the Witch drags in Jack, whom she found weeping over the Baker's Wife's body. 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 and fed up, the Witch curses and scolds them for their inability to accept their own individual responsibility and 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 killing 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 and when her Prince passes by, he nearly fails to recognize her. She confronts him, having learned of his infidelity from her birds and he explains his feelings of unfulfillment and his reasons for seducing another woman. She asks him to go, and he sorrowfully leaves.
Little Red returns with the news that her grandmother has been killed by the Giantess. Meanwhile, 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 that everyone is responsible for the choices they make, good or bad ("No One Is Alone").
The four remaining characters slay the Giant and the deceased characters now including the Royal Family (who have lost their way and starved to death in the woods) and the Princes (who have their new paramours, Snow White and Sleeping Beauty, on their arms) return to share one last set of morals with the audience. The survivors resolve to band together and rebuild. The spirit of the Baker's Wife appears to comfort her mourning husband advising her husband to tell their child their story. The Baker begins to tell the story using the same words as the narrator did at the beginning of the play as the Witch appears with the final moral: "Careful the things you say, Children Will Listen." All join in on a last reprise of the title song, surmising that we all must venture into the Woods while remembering the choices we've made and learning from each endeavor we come across ("Finale"). As the characters conclude the song singing, "Into the woods, and out of the woods and happily ever after", Cinderella closes the show with one last "I wish..."