Dr. Craven is waiting for Colin and Mary to return to Misselthwaite. Mary is taken aback by Colin's exceeding rudeness in his conversation with the doctor, and determines to bring the rudeness to Colin's attention. She tells him that everyone has always given him his own way, as they regarded him as a pitiable creature; it is to this that he owes his peculiarities. Colin is surprised by Mary's frankness, as Mary was by Ben Weatherstaff's. He tells her that he intends to cease being so peculiar, and that the "white Magic" of the secret garden will help him to do so. Mary, Dickon, Colin, and Ben Weatherstaff spend all their days in the secret garden, observing the progress of the spring. Colin and Dickon engage themselves in passionate study of the growth of the plants and the habits of the animals that live upon the moor. Colin resolves to become a great scientist, and begins with a quasi-scientific inquiry into the making of Magic. Colin summons his three companions to hear him lecture on the subject of Magic. He tells them that there is a great deal of Magic at play in the world; one need only harness it. One may see it in the work of the springtime on the garden, since "Magic is always pushing and drawing and making things out of nothing." Colin believes that he can call upon that same Magic to make him well by fervently repeating what he wishes to happen. At Colin's word, all four sit cross-legged beneath a tree, as though at a prayer-meeting, while Colin chants his desires over and over again. Colin then walks about the garden to test his newfound strength, with Mary, Dickon, Ben, and Dickon's many creatures following along behind in a kind of processional. Colin determines to keep his improving health a secret from everyone in the manor, so that his new potency will come as a complete surprise to his father upon Master Craven's return.
The garden's transformative properties take on further supernatural implications in this chapter: it is described as being a source of "white Magic," and the seeds there grow "as if fairies have tended them." This white magic, which bestows infinite goodness upon the children, is presumably to be distinguished from the "black" magic worked by the snake charmers in India. The racist implications of this distinction between white/black, good/evil, are clear. Colin's absolute engrossment in the garden and its creatures connects him absolutely into the stuff of life, and of living—he is now certain that he is going to live to be a man, and proposes that he will be the sort of "scientist" who studies Magic. Of course, the only kind of scientist who might study what Hodgson Burnett calls Magic is a Christian Scientist. Mary's chant, so similar to that of a Christian Science medical practitioner, was "a magical spell"—an instance of the simplest kind of magic. The idea that one need only "say things over and over and think about them until they stay in your mind forever" is also taken from the Christian Scientist emphasis upon the necessity of positive thinking. This religious echo is reinforced by the fact that the children's Magic circle is compared to both "a prayer-meeting" and "a sort of temple"; Colin is described as being "a sort of priest."
"Magic is always pushing and drawing and making things out of nothing. Everything is made out of Magic, leaves and trees, flowers and birds, badgers, and foxes and squirrels and people. So it must be all around us. In this garden- in all the places. The Magic in this garden has made me stand up and know I am going to live to be a man."
In this passage, Magic is again aligned with the life principle - that which is present in nature and in the springtime, in the birth of new animals (as symbolized by the robin redbreast's nest) and in the rebirth of the landscape. It is therefore not unlike the Christian God, from whom everything is imagined to issue, and who is, at the same time, described as being "everywhere." Ben Weatherstaff remarks that Mistress Craven especially loved those flowers that pointed up to the heavens: a garden, by implication, is always celestial as well as earthly. (Ben also says that Mistress Craven "[never] looked down on the earth.") The garden begins once again to swarm with roses, her favorite flower; it is as though her spirit itself is being reawakened in the garden Colin says that Mary only knows magic because she is from India, where there are fakirs, and that Dickon may know Magic but "he doesn't know he knows it." This implies that only Colin's "great scientific discoveries" will truly explain the nature of Magic; for him, it is a kind of force "like electricity and horses and steam." He thus compares Magic to three of the agents of the British Industrial Revolution; like them it may only be harnessed by the human—that is, upper-class white British male—will. Therefore, neither Mary, who is "only a girl," nor Dickon, who is "common," can truly understand Magic. Colin's improvement is maintained as the latest secret in a book that is entirely animated by secrets. He is getting well for his father's sake, in some sense: we learn that he hopes to dispel his father's hatred and fear of him with his newfound health.