In the secret garden, Colin continues to stand up straight and can even walk. Ben Weatherstaff enters the garden and Colin draws attention to himself, demanding to know from Ben if he sees him as a hunchback. Ben responds that he is not, and that everyone has been a fool to believe that Colin would die. Ben tells Colin about how the garden belonged to Mrs. Craven, his mother. Colin declares that now it is his and that it must be left a secret. Ben reveals that he has been in the secret garden before by climbing over the wall, which explains how the roses in the garden look pruned. As the sun goes down, Ben Weatherstaff presents Colin with a potted rose, which Colin plants in the soil himself.
When Colin returns for the night, Dr. Craven warns him to minimize his time spent outside, and Colin responds defiantly that he will be going out every day and that he can’t be stopped. Mary notices Colin’s rude way of ordering around people and tells him directly that he could have better manners. Colin is surprised to hear that he behaves in this strange way, but he vows to keep visiting the garden, where he will be transformed by Magic. In the following months, many magical things take place in the garden as the flowers start budding. Colin continues to spend time there every day, watching things grow. Colin believes that it is the Magic that allowed him to stand for the first time in the garden.
One day, Colin calls over Ben Weatherstaff, Mary, and Dickon to declare that when he grows up he will be a scientist who studies Magic. He proposes they do an experiment where every day they each affirm that Magic is inside of them and is making them well and to observe the results. They then sit cross-legged in a circle under the tree to start the experiment. Colin repeats a chant about how Magic lives through all of life, including in them. They then form a procession through the garden where Colin continues to declare that Magic is making him strong. He has made himself believe that he is not sick anymore and imagines what his father would think when he sees him well. The children continue to do these ceremonies regularly.
Dickon starts working at another garden near his cottage. His mother, Mrs. Sowerby, enjoys going out to this garden and talking to the boy. There, Dickon divulges to her all the things that have been happening at Misselthwaite Manor and she becomes in on the secret. Mrs. Sowerby offers to prepare the children milk and bread to enjoy during their days in the garden, in order to help Colin and Mary fatten up. Dr. Craven and the nurses are beginning to notice Colin’s increased appetite, so he can’t ask for more food. He tries to not make himself seem too healthy, as he doesn’t want anyone to find out about the secret garden and interfere with the children's daily routine.
When the doctor proposes writing to Colin’s father to tell him of his improving health, Colin panics and considers he might have to start eating less in order to discourage Dr. Craven. Mary and Colin find it difficult to eat less, however, because their appetites are growing each day. Thus they are delighted to receive the food from Mrs. Sowerby. Not wanting to put too much pressure on Dickon’s mother to feed them, they also create a tiny oven in a hollow near the garden, in which the children cook potatoes and eggs. Becoming stronger, Colin is able to stand and walk more and more. The manor staff are perplexed at how the children can grow so strong and look so healthy while eating so little.
The garden is blooming more and more and the robins are hatching eggs, which is described as a miracle. The robin’s perspective is given, where he reveals that he trusts Dickon around the eggs but not necessarily Colin and Mary. The robins observe Colin learning to walk and conclude that the boy is learning to fly. On a rainy day, Mary and Colin amuse themselves by exploring the unused rooms in the mansion. Their playing causes them to have a great appetite and they both finish their lunches for the first time in awhile, much to the happiness of the staff. Later, Mary notices that Colin has removed the curtain from his mother’s portrait in his room.
Colin continues to lecture the children and Ben Weatherstaff about Magic, even while they are at work weeding in the garden. One day, Ben suggests Dickon sing the “Doxology,” a hymn which praises God and all His creatures. As the children sing the hymn, a woman with affectionate eyes and a long blue cloak enters. It is Dickon’s mother. She is surprised and happy to see Colin so well. She is also shocked because of the uncanny resemblance Colin bears to his own mother. She also notices how much Mary has grown healthier. The children ask her if she believes in Magic, to which she says yes, calling it the “Big Good Thing” in which they must always put their faith.
The last chapter starts with narration about how the power of thoughts will be discovered and better understood in the 20th century. For instance, a bad thought can negatively affect the body just as much as a disease. This is shown through the characters of Mary and Colin. The narrator speaks of Mr. Craven, who for 10 years has thought only negatively and has not had the courage to be more positive, even while traveling throughout beautiful places in Europe. One day, while sitting by a stream in Austria, he starts thinking of the site’s beauty and he suddenly feels alive for the first time in years. He can’t maintain this new hope all the time, but he feels over the next few days that his usual sense of burden periodically lifts.
One night, Mr. Craven dreams of hearing Mrs. Craven’s voice calling to him, telling him that she is in their special garden. The next day, he receives a letter from Mrs. Sowerby advising him to come home, and that Mrs. Craven would want him to come if she were alive. Mr. Craven makes the journey back, thinking of Colin in a way he hasn't in years. He reflects on how he has not been the best father to Colin, avoiding him because of his resemblance to his wife. As he arrives back at the manor, he thinks about how he will find the key to the secret garden. Mrs. Medlock updates Mr. Craven on Colin’s new behaviors and habit of going outdoors every single day.
Mr. Craven hurriedly goes to the secret garden. Outside its walls he is surprised to hear commotion and laughter of children. All of a sudden, Colin bursts out of the garden door and bumps directly into his father. Mr. Craven is astonished yet happy to see Colin standing, looking healthy and vibrant. Colin takes him into the garden and tells him everything: about the Magic, the creatures, and his new friends. Mr. Craven laughs and cries with joy at hearing his son’s story. The manor servants are completely shocked when they see out the window a healthy-looking Colin and his father walking together towards the house.