The Narrator begins the story
 by guiding the company through each character's wish ("Opening Parts 1 - 9"). Cinderella wishes to go to the King's Festival; Jack wishes his cow, Milky-White, would give him milk; and the Baker and Baker's Wife wish to have a child. Jack's Mother wishes for gold and a less foolish son. Since their cow won't produce any milk, she insists that Jack take the cow
 to market to sell her. Cinderella's Stepmother and her stepsisters, Florinda and Lucinda, laugh at Cinderella's wish. With Cinderella's Father, they ride off to the ball without Cinderella, leaving her behind in tears. After stopping at the bakery for sweets, Little Red Ridinghood prepares to travel into the woods to see her sick Granny.

At their home, the Baker and his Wife are visited by the Witch next door. She reveals that the Baker's father is the reason the couple's wish will never come true. She explains that, in the past, for his pregnant mother, the Baker's father stole magical beans from the Witch's garden. To punish them, the Witch placed a curse on the family, guaranteeing none would ever bear children again, including the Baker and his Wife. Once born, the Witch took the Baker's sister (a sibling that he never knew existed) and hid her in a tower far, far away. In order to break the spell and get his wish, the Witch tells the Baker he has three days to bring her four items: a cow as white as milk, a cape as red as blood, hair as yellow as corn and a slipper as pure as gold.

As the Baker prepares for his journey, he puts on his father's old jacket and finds six beans in the pocket. Forbidding his Wife to join him on the quest, he tries to memorize the list of things the Witch has asked for. At the grave of Cinderella's Mother, Cinderella shares her wish and is granted a beautiful dress and slippers to wear to the ball ("Cinderella at the Grave"). While walking through the woods to market, Jack encounters a Mysterious Man who says his cow is worth only a sack of beans. Little Red Ridinghood meets a Wolf who targets her and her grandmother for his next meal ("Hello, Little Girl"). We hear the voice of the Baker's lost sister, Rapunzel, singing in the distance ("Underscore after 'Hello, Little Girl'").

As the Baker struggles to remember the four objects on his list, his Wife persuades Jack to sell Milky-White to her for five of their beans. After Jack's sad farewell, the Baker's Wife tries to allay the Baker's guilt by insisting they did Jack a favor ("I Guess This Is Goodbye/Maybe They're Magic").

The Witch visits Rapunzel at the tower where she is kept prisoner ("Rapunzel"). Rapunzel's Prince sees the Witch climb Rapunzel's hair and decides to try it himself the following day.

The Baker unsuccessfully tries to take Little Red Ridinghood's cape ("Baker's Reprise"). She enters her Granny's house to find the Wolf in bed, pretending to be the old woman (whom he has eaten). He gobbles up Little Red Ridinghood and falls asleep. The Baker, hoping to get the cape, cuts the Wolf's stomach open, releasing Little Red Ridinghood and her Granny. After the ordeal, Little Red Ridinghood realizes how naive she was ("I Know Things Now") and gives the Baker her cape as a gift for saving her life.

Jack's mother is furious with 
him for selling their cow for five worthless beans and throws them away. The Baker's Wife leads Milky-White through the forest when she encounters Cinderella, who is running from Cinderella's Prince and his Steward. Cinderella isn't sure she wants the Prince, and the Baker's Wife thinks she is a fool ("A Very Nice Prince"). Seeing Cinderella's gold shoes, the Baker's Wife tries to take one but is forced to chase after the runaway cow as the final chime of the first midnight is heard.

The next morning, Jack discovers 
a beanstalk has grown overnight. As the Baker sleeps beneath a tree, Jack appears with an oversized sack full of money, singing about giants ("Giants in the Sky"). Jack's Mother, delighted by his acquisition, has let him keep five gold pieces, which he uses to try and buy back Milky-White, but the Baker cannot sell the cow because he needs it for the Witch. Jack, thinking the Baker wants more money, goes back up the beanstalk in search of additional funds. The Baker's Wife appears, confessing she has lost the cow.

Rapunzel's Prince and Cinderella's Prince exchange tales of woe ("Agony"), each insisting his romantic problem is more serious than his brother's.

The Mysterious Man returns the cow to the Baker. The Baker's Wife, recognizing Rapunzel's hair as the perfect shade to satisfy the Witch's demands, rips out one of the girl's substantial tresses ("Rapunzel's Reprise") and runs into Cinderella, who is on her way home from another night at the Festival. The Baker's Wife tries again, without success, to take Cinderella's shoe. The Baker finally agrees to accept his Wife's help, realizing it will take both of them to accomplish their goal ("It Takes Two"). Jack returns to the Baker with a golden egg that he offers in exchange for Milky-White when, all of a sudden, the cow lets out a terrible yelp and falls to the ground dead.

With two midnights gone, the Baker goes in search of another cow. Meanwhile, Rapunzel is defiant and tells the Witch that she wants to see the world. After warning Rapunzel to obey her ("Stay with Me"), the infuriated Witch cuts off most of Rapunzel's hair and exiles her. The Narrator reveals that, while pursuing Rapunzel, her prince has fallen into a patch of thorns and blinded himself.

Leaving her third visit to the royal ball with only one slipper, Cinderella reflects on her indecision about departing her miserable home for the unknown aspects of life with the Prince ("On
 the Steps of the Palace"). To help her continue to run from the Prince, the Baker's Wife gives Cinderella her own shoes in exchange for the remaining gold slipper.

The Baker and his Wife report to
 the Witch with their four objects. After rejecting the new cow — that is not actually white, but just covered with flour — the Witch demands they bring the dead Milky-White to her. She restores the cow to life and commands the Baker
 to feed the cow the other objects, insisting that it be milked to fill a silver goblet. Jack tries, but no milk flows ("The Potion Part 1"). When the Baker's Wife says she pulled the hair as yellow as corn from a maiden in 
a tower, the Witch explains she, the Witch, cannot have touched any of the objects needed to break the spell. 
The Mysterious Man, revealed to be
 the Baker's father, suggests feeding
 the cow the hair from an ear of corn. The cow fills the goblet with milk that the Witch drinks, transforming her into a beautiful woman ("The Potion Part 2"). As the third midnight strikes, the Baker's father dies and Milky-White is reunited with Jack. The Prince finally finds his Cinderella and Rapunzel, reunited with her Prince, restores his vision with her tears. The Witch realizes that, in exchange for her own youth and beauty, she has lost her magical power over others.

Having broken the curse, the Baker's Wife is happily pregnant, and the Narrator observes that the kingdoms are now filled with joy. We are reminded there will be times when each of us must journey into the woods but that we must mind the future and the past ("Finale Parts 1 - 6").