The book opens by introducing Mary Lennox, a sour and disagreeable 9-year-old girl. She lives in India with her father, a British statesman, and her mother, a self-absorbed woman who frequently is out at parties and socializing. Mary has been mostly raised by her Indian servant named Ayah. Ayah and the other servants are extremely docile and will indulge Mary’s every whim, which has led her to become a very spoiled little girl who expects others to do everything for her.
One day, there is news of a cholera outbreak and Mary finds out abruptly that her nurse Ayah has died. She does’t feel much sadness and goes to take a nap. Later she is found by a police officer who tells her that both her parents have also perished from the disease. As a result, Mary is sent to live with her uncle, Archibald Craven, at his huge estate in Yorkshire, England. The estate is called Misselthwaite Manor.
Mary journeys to England by boat and is met by Mr. Craven’s housekeeper, Mrs. Medlock. Mary continues behave very disagreeably, feeling a reluctance to move to this unknown place. In the car ride to the manor, Mary is informed by Mrs. Medlock about her uncle’s reclusive behavior. Mr. Craven has become somewhat of a hermit after losing his beloved wife 10 years prior. When they arrive at the mansion, Mary is sent straight to her new room and meets her servant, Martha Sowerby.
In the first few days after arriving at the manor, Mary must acclimate to her new environment. She realizes that the servants in Yorkshire behave quite differently from those in India; Martha, for instance, refuses to dress Mary and instead encourages the little girl to be more independent. For the first time in her life, Mary must use her own imagination and is left to play outside in the massive gardens. There she meets a groundskeeper named Ben Weatherstaff, who is initially gruff yet gradually starts to warm up to Mary. Ben introduces Mary to the garden robin, who is very friendly and likes humans.
Mary, while playing by herself in one garden, enjoys the company of the robin and is glad to at last feel much less lonely. She is able to reflect upon her isolation and laziness while living in India, where she would never go out to have adventures or meet friends. One afternoon she discovers a garden with a wall but a locked door. Martha later explains that this garden has been closed by Mr. Craven, because it was the favorite garden of Mrs. Craven and also the place where she tragically died after being hit in the head by a tree branch. Mary feels curious about the garden and later finds the key to it.
Mary slowly starts to open up and become healthy, eating more food and feeling finally that the “cobwebs” are being dusted from her mind. She uses the key she found to enter the secret garden and is delighted by its beauty, despite 10 years of neglect. She feels instantly protective of the special place and desires to keep the garden alive. When she makes friends with the personable and kind-hearted Dickon Sowerby, the brother of Martha, she asks the boy to help her revitalize the garden, and he agrees. They also agree to keep their activities in the garden a secret, so that Mr. Craven and his staff do not find out and ruin their fun.
One day, Mary is finally called into the office of Mr. Craven and meets him face to face. She immediately notices how he seems incredibly unhappy and not fully present. Although he is kind to Mary, she can tell his mind is on other things. He tells her that he will be away for months traveling and that she is free to play outside, without supervision. This delights Mary, who was inwardly worried that he would assign her a governess, making it impossible for her to continue her work in the secret garden.
In the following days, she hears several times a strange crying noise at night in the mansion, as if from a child. The other servants in the house deny that there is any noise, but Mary is sure of what she hears. One day she goes to discover what the sound is herself, looking through the numerous bedrooms of the mansion. Finally she finds that the crying is coming from one bedroom, where there is a little sickly boy in a bed. The boy is Colin Craven, the 10-year-old son of Mr. Craven and Mary’s cousin.
Mary finds out that Colin has been purposefully hidden by his father, as his presence is another painful reminder of Mrs. Craven’s death. Colin has been told his whole life that he is sickly and will not live very long, and for this reason he is also quite disagreeable and often throws temper tantrums. This behavior reminds Mary of herself in India and she tries her best to show compassion to Colin, meeting with him often and entertaining him with stories about her life in India. She also tells him about the secret garden, which perks Colin’s interest.
Eventually, Mrs. Medlock catches Mary in Colin’s room and is angry and worried that he has been discovered. Yet quickly the servants are happy that Mary has befriended Colin, for she is the only one able to soothe the boy when he throws a tantrum. After one major incident of crying and screaming, Mary helps Colin by bluntly telling him that he creates his own malaise through his negative thoughts and beliefs about himself. Colin is able to snap out of it and from this moment on starts on a path of healing and reencountering his childhood.
Mary introduces Colin to Dickon, and the three of them secretly visit the garden and continue to work on planting and nurturing it, along with the help of Ben Weatherstaff. The garden becomes their favorite and most treasured place, where they spend each day enjoying nature. One time, Ben Weatherstaff gives Colin roses—the favorite flower of his mother—to plant in the secret garden. This moment marks when Colin shifts his attitude towards his mother into a more positive one, whereas before he blamed her for all his sickness and isolation.
As the days go by, the children together discover the presence of magic in the garden and are enlivened with a new appreciation for life, especially Colin. Colin leads the others in chants where they affirm that magic lives inside of them. With this newfound self-confidence, Colin starts to feel much better and is even able to walk after years of being chair-bound. Both Mary and Colin gain weight and transform out of their sickly and sullen former selves. The staff—who have forever known Colin to be poorly behaved and disinterested in playing outside—are very perplexed by this development.
In the final chapter, we are brought to a scene where Mr. Craven is sitting by a river in Austria. In a very magical way, he is suddenly able to feel happy and at peace—a rare sensation after years of grief and depression. Then, that night he has a dream about Mrs. Craven beckoning him to come into the secret garden. These two events propel Mr. Craven to stop his travels and return to his manor. Upon arriving, he goes straight to the secret garden, only to find the children there. He is shocked to see them, especially his own son Colin enjoying himself and walking like a normal child. Father and son are reunited and reconcile. In the final scene, they walk together into the house while the servants look on in disbelief.
