Mary Lennox, a ten-year-old girl who loses her parents to a cholera epidemic in India (“Opening Dream”), is sent to live with her uncle Archibald Craven, at Misselthwaite Manor in England (“There’s a Girl”). He is the widower of Mary’s Aunt Lily who died many years earlier. He is a hunchback and is still grieving over his wife’s death.
His brother, Dr. Neville Craven, is largely responsible for the management of the manor, along with the housekeeper, Mrs. Medlock. Mary receives a cold welcome upon arrival (“The House Upon the Hill”), and she has trouble sleeping her first night (“I Heard Someone Crying”). She, Archibald, Lily, and the Dreamers lament the loss of loved ones.
The next morning Mary meets Martha, a young chambermaid, who tells her about the grounds, a hidden garden in particular, and encourages her to play outside (“If I Had a Fine White Horse”). Meanwhile, Archibald reminisces about how he met Lily (“A Girl in the Valley”).
As Mary explores the grounds, she meets Ben Weatherstaff, the head gardener, and Dickon, Martha’s brother. Through a series of songs (“It’s a Maze,” “Winter’s on the Wing,” and “Show Me the Key”), Mary learns the history of the hidden garden and its lost key. She befriends a robin who shows her the location of the missing key, but not the door.
Neville tries to persuade Archibald to send Mary away to school and for him to find happiness elsewhere, if not at Misselthwaite. Archibald resists, and meets with Mary, who asks him for “A Bit of Earth.” As a storm approaches (“Storm I”), both Archibald and Neville realize how much Mary reminds them of Lily (“Lily’s Eyes”), with whom both men were in love.
In her wanderings throughout the manor, Mary again hears someone crying (“Storm II”) and discovers Colin, her bed-ridden cousin. She learns that his mother Lily died when Colin was born and he is terrified that he, too, will become a hunchback like his father. He tells her of his dreams about “A Round-Shouldered Man” who takes him on adventures.
As the children are becoming friends, Mrs. Medlock and Neville enter and angrily threaten Mary to stay away from Colin. In her frustration, she rushes outside into the climax of the storm, and with the help of the Dreamers, finds the door to the garden (“Final Storm”).
Mary envisions having a secret place to go to be herself (“The Girl I Mean To Be”), but Neville is again campaigning to have her sent away to school because she is disrupting his “treatment” for Colin. Archibald again refuses and relates a dream he had of Lily and Mary together in the garden. The brothers individually reflect on Lily, while a flashback shows Rose, Mary’s mother, and Lily arguing over the forthcoming marriage of her and Archibald (“Quartet”).
Archibald finally permits Neville to investigate a few schools for Mary and leaves for Paris, stopping to look in on the sleeping Colin (“Race You to the Top of the Morning”).
By this time, Mary has found the door to the garden but believes everything inside to be dead. Dickon tells her that the garden is just dormant and offers his help in waking it up (“Wick”). Mary tells Colin about the garden and tries to convince him to come outside to see it. He is reluctant until he has a vision of his mother inviting him to her garden (“Come to My Garden/Lift Me Up”).
Late one night, Mary, Dickon, and Martha covertly bring Colin to the garden in a wheelchair. As they spend time there the exercise and fresh air help Colin regain his health (“Come Spirit, Come Charm”). The Dreamers share in the joy of the moment (“A Bit of Earth (reprise)”).
Not long after, Mary is in danger of being sent away to boarding school by Neville (“Disappear”), but is buoyed up by Martha who tells her to “Hold On” to everything and everybody to which she has grown close. She writes to Archibald and asks him to come home (“Letter Song”).
In Paris, Archibald still struggles to find peace in his life (“Where in the World”), but Lily’s ghost persuades him to return home to Misselthwaite Manor (“How Could I Ever Know”). Entering the garden on his arrival, he discovers Colin in complete health, running and playing with the others. Archibald, now a changed man, invites Mary to be his own, and the Dreamers bid all to “stay here in the garden” (“Finale”).