Colin Craven's absolute engrossment in the garden and its creatures fuses him absolutely with the stuff of life, and with the work 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—throughout the novel, the idea of magic is heavily inflected by the tenets of both Christian Science and New Thought. One definition of magic that the novel provides is the conception of magic as a kind of life force—it enables Colin stand, and the flowers to work out of the earth. It is also aligned with the Christian God, in that Colin says that the Doxology (a Christian hymn) offers thanks to the same thing he does when he says that he is thankful for the magic. This Christian connotation is strengthened in a number of ways, among them in Mrs. Sowerby's description of magic as a kind of creator, who is present in all things, and even creates human beings themselves—clearly associating him with the all-powerful, all- knowing, and omnipresent Christian God. Christian overtones can also be found in the scene in which Mary throws open the window so that Colin may breathe in the magical springtime air. Colin's half-joking suggestion that they may "hear golden trumpets" recalls the golden trumpets that are believed by Christians to herald the entrance into Paradise. Furthermore, Mary says that the spring air makes Dickon feel as though "he could live forever and ever and ever"; this idea clearly echoes the Christian belief that Paradise contains the promise of eternal life. Unlike conventional Christian myth, Paradise can be found on earth, in nature, as well as in heaven. This shift mirrors that made by Hodgson Burnett's system of New Thought, which held that divinity could be found in the landscape, in all natural living things. Colin again shouts that he feels that he will live forever directly before the singing of the Doxology. 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." The chanting they perform to call upon the healing properties of the magic is very similar to the healing prayers of a Christian Science medical practitioner. 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 power and necessity of positive thinking.
One of the book's underlying themes is the way in which happiness begets happiness, and misery begets only more of itself. For example, the fact that Master Craven is sad ensures that he will continue to be sad, and will make those around him similarly dismal. The source of this notion can again be found in Burnett's fascination with the New Thought and Christian Science movements, which held that one must think only positive thoughts if one wants good things to happen. The fact that this idea is patently false miraculously did nothing to deter its adherents. Dickon's remark that "the springtime would be better [for Colin] than doctor's stuff" provides another instance of Christian Scientist tenets in the novel. Christian Science, as a philosophy, disapproves of medical intervention: no disease is truly corporeal (caused by the body), but is in fact the result of morbid and negative thinking. Colin must have contact with the life of the world if he is to go on living, because this contact will dispel his thoughts of death: Dickon (guided by Burnett's Christian Scientist beliefs) says that Colin "oughtn't to lie there thinking [of death and illness]... No lad could get well as thought them sorts of things." The fact that Colin's fury at Ben Weatherstaff provides him with sufficient strength to stand reinforces the notion that his previous inability to do so was entirely a product of his negative thinking. It also underlines the idea that if one only wishes to overcome one's illness, one can. Negative thoughts are the human error to be found at the root of all disease; one must therefore force out ugly thoughts with agreeable ones, for "two things cannot be in one place." This notion is responsible for both Colin and Mary's wondrous metamorphoses. Once they are thinking of the garden and nature, of Dickon and of their own blossoming friendship, they can no longer concern themselves with their own contrariness or with the fear of becoming a hunchback and dying an early death. Instead, they become normal, healthy children, full of dreams of the future. This questionable (and inarguably syrupy) goal is given inane epigraphic expression in the phrase "Where you tend a rose, my lad, a thistle cannot grow."
One of the most important ways that the novel illustrates this theme is by creating an opposition between India and England. The novel subtly attributes Mary's childhood sickness to her time in India: "Her face was yellow because she had been born in India and had always been ill in one way or another." India, clearly, is no place for an English child (though the novel seems to suggest that the fault for this lies with India, rather than with the British invasion of that country). India is consistently presented as a place which breeds illness and unbeauty, as well as a kind of living death: so long as Mary lived there, she was "always too hot and languid" to do anything at all. Her time on the moor begins to effect a change in Mary: she slowly begins to grow stronger and healthier, and her imagination, which had lain dormant during her time in India, is quickened by her exploration of the manor grounds and her search for the secret garden. Her contact with English gardens, English boys, and English moors cures her of her Indian malaise. Similarly, Master Craven's constitutional sickness is further borne out by his constant travel "in foreign places." In the economy of the novel, all life and joy are contained on Missel Moor, and thus to travel is a sign of illness. To leave the moor is to condemn oneself to suffering. Travel, the narrator announces severely, indicates that Master Craven has "forgotten and deserted his home and his duties." The natural landscape is consistently depicted as conspiring with and mirroring its human inhabitants: it is the "wuthering" (howling) of the wind that awakens Mary and alerts her to Colin's crying; the robin redbreast and a timely gust of wind reveal the key and door to the secret garden to her. The natural landscape is subject to personification (the lending of human attributes to a nonhuman creature or inanimate thing) throughout the novel. The secret garden resurrects Colin and Mary, and they resurrect it in turn.
Susan Sowerby's comment that children who are unwanted never thrive is another permutation of the Christian Scientist idea that no disease is truly corporeal (caused by the body), but is in fact the result of morbid and negative thinking. Since both Colin and Mary were not loved, and both had childhoods surrounded by a great deal of anxiety and negative thinking, it is almost as though their parents wished that they would fall ill. Furthermore, Colin and Mary are so bitter and selfish because they are lonely and utterly without friendship: they require the company of other children to check their selfish impulses and inspire their innate kindness. The instant they begin to attach themselves to each other, to Dickon, and the natural world, they become kinder and more sympathetic.