Mary passes a number of weeks in which each of her days is like the others: she awakens, eats breakfast, and then wanders the moor all day. Her time out of doors begins to cause a change in her: she slowly begins to grow stronger and healthier, and her imagination, which had laid dormant during her time in India, is quickened by her exploration of the manor grounds and her search for the secret garden. Outside one of Misselthwaite's walled gardens, Mary has a second encounter with Ben Weatherstaff's robin. She is terribly pleased to see him, and chases after the robin as he flies along the garden wall—she even goes so far as to chirp and whistle at him, even though she does not know how. In her pursuit of the robin, she becomes certain that he lives in the secret garden. She cannot, however, find its door. That night, Martha tells Mary further stories of the secret garden, even though Master Craven has forbidden the servants to discuss it. The garden once belonged to Mrs. Craven, and she and her husband had spent many intimate hours there in the years of their marriage. It had been Mrs. Craven's custom to sit in a rose-covered bower at the top of one of the garden's trees, and, one day, she fell from it when a branch gave way. She died of her injuries, and, after her death, Archibald Craven could no longer bear the garden and had it locked shut. Hearing this story, Mary feels a great pity for her uncle. As she listens to the wind blowing over the moor, she is able to discern another sound beneath it: the sound of someone, a child, crying. Martha denies hearing any such sound, though Mary does not believe her.
The following day, a rainstorm keeps Mary indoors. She realizes that she is beginning to like both Martha and her stories of her family, and feels an affinity with both Dickon and Martha's mother, though she has never met either of them. To keep herself occupied despite the rain, Mary sets out to search for Misselthwaite's library, and to explore its hundreds of shuttered rooms. She is not concerned that anyone will try to stop her, because no one in the manor much troubles themselves with her. In Yorkshire, unlike in India, Mary must fend for herself. As she walks through the manor's corridors, Mary notices many portraits of grand, antique-looking men and women hanging upon the walls; their faces seem to wonder at how a girl from India came to live on their estate. She is much interested in the portraits of children, and even speaks to one of a girl who looks like Mary herself: the girl is curious-looking, and a green parrot is perched upon her finger. Mary wishes the girl in the portrait were there to keep her company; she feels that there is no one at all alive in Misselthwaite save for herself. Upon entering one of the rooms that open onto the corridor, Mary finds yet another portrait of the girl who looks so like her. The girl's stare unnerves her, and she leaves to explore a number of other rooms, stopping finally in one that might have once been a lady's sitting room. There, Mary happens upon a collection of ivory elephants; as she knows all about both ivory and elephants from her life in India, she is quite taken with them. Suddenly, she hears a soft rustling sound behind her, and turns to find a family of gray mice living in one of the room's velvet cushions. Mary thinks to herself that, though the mice and she may be the only living things in the manor at that moment, the mice, having each other, are not lonely at all. Upon going back into the corridor, Mary again hears a child's cry; when she goes off in search of its source, she is apprehended by a furious Mrs. Medlock, who takes her back to her room.
The fifth chapter opens by detailing the restorative effect the moor has begun to have upon Mary: she has started, in the words of the book, to "wake up." Mary's curiosity about the secret garden is presented as both the most important symptom and the most vital cause of her newfound alertness. The pivotal opposition between wakefulness and sleep is reinforced here, with the former being aligned with England and the latter with despised India:
[The garden] gave her so much to think of that she began to be quite interested... In India she had always felt hot and too languid to care much about anything. The fact was that the fresh wind from the moor had begun to blow the cobwebs out of her young brain and waken her up a little.
Throughout The Secret Garden, both climate and landscape are presented as having a determining influence upon one's health and well-being; that is, one can only be truly healthy by being in harmony with one's environment. This motif comes out of Hodgson Burnett's own fascination with the Christian Science and New Thought movements, which held that the natural landscape was suffused with the spirit of the Christian god, and thus had healing capacities. This idea will recur ceaselessly throughout the novel and is, in large part, its central motif. Another way in which the novel reworks common Christian myths can be found in its positioning of the secret garden as a kind of Eden. Eden was the garden in which the first humans created by God (Adam and Eve) lived until God cast Adam and Eve out of the Garden of Eden for tasting the fruit of the tree of knowledge. The secret garden is connected with Eden through Martha's story of the divine times had there by Master Craven and his wife before her quite literal fall—before, that is, she fell out of the rose-tree to her death. Master Craven's fanatical insistence upon secrecy is here revealed to extend even further than the reader first suspected: the servants may not talk of his wife nor of her death, nor of the garden, nor of the strange cries that Mary hears in this chapter for the first time. His prohibition is utterly disregarded by Mary (thus providing further evidence of her "contrariness"). Her voyage through the great house reinforces the book's uncanny fairy-tale quality, in that it seems to Mary that the "hundred rooms" have always stood empty; furthermore, the very paintings on the walls seem to follow Mary with their eyes, and one seems to be of Mary herself, as she would have looked if she had lived one hundred years before. Mary's discovery of the ivory elephants and frightened family of mice in the abandoned bedchamber provides yet another example of the opposition between India and England. India, here represented by the elephants, is stony, chill, and lifeless; England, represented by the wide-eyed mice in the velvet cushion, promises life and companionship. Mary's fascination with Dickon and with Martha's mother, Mrs. Sowerby, also increases in this chapter. Her interest in these two arises, in some measure, out of her own motherlessness: she imagines that Mrs. Sowerby might "comfort" her, as her own mother never did. Dickon, in this chapter, is described as being a caretaker of motherless things: Martha mentions that he has a pet fox-cub and a pet crow, both of whom he saved after the deaths of their mothers.