That night, the sound of the rain drumming upon the windows awakens Mary. She is greatly miserable at the onset of the storm, because she knows that it will keep her confined to the manor house all the following day. Once so awakened, she is too upset to go back to sleep. The wind and rain sound to Mary like human wails-"like a person lost on the moor and wandering on and on crying."

After lying awake for nearly an hour, Mary hears something beneath the sound of the storm: the same cries she heard in the corridor, as of a child weeping. In complete defiance of Mrs. Medlock's command that she keep to her room, she goes off in search of its source. Mary follows the noise through Misselthwaite's darkened corridors, until she finds the door to a room in which a light is still burning.

Upon entering the room, Mary finds a thin, curious-looking boy lying upon a massive four-poster bed. The boy is as white as a statue, as though he has been ill, and he is crying. Each child is not certain whether the other is a ghost, or a dream, and, for a long while, they simply stare speechlessly at one other. The boy is Colin Craven, Master Craven's son. He was born ten years before, in the same year in which Mary was born and the secret garden locked shut. Colin's father cannot bear to see him, as Colin reminds him of his late wife; the boy resembles her, and was born only shortly before she died. Archibald is ashamed of how sickly Colin is, and has forbidden the servants to speak of him. Everyone fears that he will become a hunchback and die before he reaches adulthood. Colin himself hates to be looked at, because he despises the pity and morbid fascination he inspires. He refuses to leave the manor house, and spends all his time shut up in his grand gloomy room. Colin does not mind, however, if Mary looks at him, as he is greatly interested in who she is and where she comes from. Mary is only too happy to stay in the hidden room and talk to the hidden boy—both remind her of the secret garden. Colin tells Mary that his father gives him anything he wants to amuse himself with; everyone must obey his wishes, as it "makes [him] ill to be angry."

When Mary mentions the secret garden to Colin, he begins bombarding her with questions. He threatens to force the servants tell him everything they know about the garden, and calmly states again that everyone must obey his wishes, as he may one day be master of Misselthwaite-provided that he lives.

To distract him from the question of the garden, Mary asks Colin if he truly believes that he will die. Colin tells her that he imagines that he will, for people have been saying that he will not live to adulthood since his birth. Colin's doctor is Archibald Craven's brother, and it would suit the doctor well if Colin died, since the manor would then belong to him. It was the thought of his impending death that caused Colin to weep.

Colin tells Mary that he wants to see the secret garden more desperately than he has ever wanted anything, and that he intends to make the servants take him to it. Mary anxiously replies that the garden will be utterly spoiled if everyone knows of it. It is glorious because it is a secret. Colin, who has never had a secret before, agrees to keep this one.