The novel begins by introducing the reader to Mary — although it would perhaps be more accurate to say it begins by introducing us to her faults. She is described as ugly, ill-tempered, and viciously demanding; in short, she is "as tyrannical and selfish a little pig as ever lived." At the same time, however, the reader is given to understand that the source of Mary's hatefulness is not precisely in her: the blame lies with her parents—particularly her mother. Disappointed by her daughter's ugliness and sickliness, Mary's mother cruelly refuses to see her, instead leaving her in the care of a retinue of Indian servants who care nothing at all for the child. The servants must, however, obey her every whim, in this can be found the source of her imperiousness. Mary's only pleasure, even at this early point in the novel, is play-gardening: she sits beneath a tree and idly places cut flowers in mounds of sound. After the death of her parents in the cholera epidemic, she engages in the same activity at the house of the clergyman and his family. Throughout the first part of the novel, Mary remains standoffish and rude; however, the omniscient narrator consistently makes it clear that Mary is only so awful because of the wretched circumstances of her early childhood. The reader has access to the loneliness and displacement that Mary herself is not able to express, but feels deeply. The instant her circumstances improve—that is, the instant that she arrives at Misselthwaite—Mary too begins to improve. She becomes active and interested in the world around her (in India, she was always "too hot and languid to care about anything.") The reader thereby recognizes that there is nothing innately cruel about Mistress Mary: she is a victim of her own isolation. Mary develops real affection for her maidservant, Martha Sowerby, and for the robin redbreast that lives in the secret garden. She falls thoroughly in love with Dickon, and befriends Colin and Ben Weatherstaff; in short, she becomes utterly engrossed in the world around her. The English landscape and her work in the secret garden have a miraculously restorative effect upon her: by novel's end, Mary is no longer bitter and friendless, but is instead an ordinary playful ten-year-old girl surrounded by her intimates.

So long as Mistress Mary's mind was full of disagreeable thoughts...she was a yellow-faced, sickly, bored and wretched child...When her mind gradually filled itself with robins...with springtime and with secret gardens coming alive day by day, and also with a moor boy and his "creatures," there was no room left for the disagreeable thoughts...[and so she became well and happy].

In the world of The Secret Garden (heavily influenced as it is by Christian Science and New Thought), one need only fill one's mind with positive thoughts to change one's fortunes. Divine nature, in the form of Dickon and the secret garden, makes this possible for both Mary and Colin.