Protagonist Mary Lennox, "as tyrannical and selfish a little pig as ever lived," is nine years old when she wakes one morning in India to an empty house, forgotten by all in the chaos of a cholera epidemic that has killed her pretty young mother, British army captain father, and most of their servants. The novel charts Mary’s removal to England and her physical, psychological, and moral development on the Yorkshire estate of her widowed uncle Archibald Craven, a reputed "hunchback." As part of her own maturation, Mary catalyzes growth and healing in (and between) her mildly spinally disfigured uncle and his "invalid" son Colin.
The secret garden of the title is Mary’s aunt Lilias’s creation. It has been virtually abandoned since the accident that resulted in Colin’s premature birth and Lilias’s death. Colin himself, while overprotected by the servants, is ignored by his depressed father and hidden in the estate. Mary discovers and rehabilitates both the secret garden and her secret cousin with the help of the working-class Sowerby family, including the servant Martha, her brother Dickon (a boy in tune with nature), and their mother Susan. Archibald, travelling across Europe to escape his sadness, is called back to the garden by a dream of his dead wife and returns to find Colin healthy and walking.