As Mary is exploring the periphery of the gardens, her robin friend draws her attention to an area of turned-over soil. Mary finds the key to the locked garden, and eventually the door to the garden. She asks Martha for garden tools, which Martha sends with Dickon, her twelve-year-old brother. Mary and Dickon take a liking to each other, as Dickon has a kind way with animals and a good nature. Eager to absorb his gardening knowledge, Mary lets him in on the secret of the garden.
That night, Mary hears the crying again. She follows the noise and, to her surprise, finds a small boy her age living in a hidden bedroom. His name is Colin. She soon discovers that they are cousins: he is the son of her uncle, his mother died when he was a baby, and he suffers from an unspecified spinal problem. Mary visits every day that week, distracting him from his troubles with stories of the moor, Dickon and his animals, and the garden. Mary finally admits she has access to the secret garden, and they decide Colin needs fresh air. Colin is put into his wheelchair and brought outside into the garden, the first time he has been outdoors in years.
While in the garden, the children are surprised to see Ben Weatherstaff looking over the wall on a ladder. Startled and angry to find the children there in Colin's mother's garden, he admits he believed Colin to be a cripple. Colin stands up from his chair and finds that his legs are fine, though weak from disuse for so long.
Colin spends every day in the garden. The children conspire to keep Colin's recovering health a secret so he can surprise his father, who is travelling and still mourning his late wife. As Colin's health improves, his faraway father sees a coinciding increase in spirits, culminating in a dream where his late wife calls to him from inside the garden. When he receives a letter from Martha's mother, he takes the opportunity to finally return home. He walks the outer garden wall in his wife's memory, but hears voices inside, finds the door unlocked, and is shocked to see the garden in full bloom, including his healthy and invigorated son. The servants watch, stunned, as Mr. Craven walks back to the manor and Colin runs beside him.this, and Mary takes to it immediately. Mary occupies her time wondering about both the secret garden and the cries she hears at night. The servants claim not to hear the cries.