The novel begins with the main character, Michael, and his family moving in to a new house. The house used to belong to an old man who died in it and wasn't found for a week. Michael's father tries to repair and clean the dangerous garage as best he can, but the garage is so dilapidated that Michael's father warns him not to go inside. Meanwhile, his mother is often at the hospital caring for Michael's baby sister who has been born prematurely.
One day when Michael goes in to the garage, amid all the boxes and debris, and dead insects, he finds a strange human-like creature called Skellig who seems to have almost wasted away. At first Michael is not even sure the creature is real or a product of his imagination. At school, Michael learns that human shoulder blades could be vestigial wingtips, which leads him to suspect that all humans could be descended from angels and that Skellig himself might be an angel because of some strange growths on his back.
Michael continues to look after Skellig and takes him food. Skellig is crotchety and arthritic, demanding aspirin and brown ale. Meanwhile, his friends from school become more and more distant when Michael spends less time with them. He also meets a girl around his age named Mina who lives next door. She is home schooled, and is very interested in nature and poems by William Blake (her parents introduced her to his work). She takes care of some baby birds who live in her yard. As Skellig becomes accustomed to and more tolerant of Michael, Michael decides to introduce him to Mina. The two children move Skellig out of the garage and into an abandoned house. They discover that he has wings, although they are dry and folded up and that Skellig is actually quite a young man, opposed to the image the author had created in the first few chapters.
Michael learns more about arthritis, even visiting patients in the hospital where his baby sister is being treated. He tries to help Skellig overcome his ambiguously spiritual as well as physical illness. Skellig begins to heal and become what would appear to be an angel. The owls, whose company he has enjoyed while living in the old house, take him mice to eat. He gives Michael and Mina a mystical experience in which they can see ghostly wings sprouting from each other's shoulder blades.
But then, Michael's baby sister comes dangerously close to death. His mother goes to hospital to stay with the baby and pray over her. That night something mysterious happens and her mother dreamt of seeing a man come in and pick up the baby. Skellig disappears, and the baby survives. Even with Skellig gone, Michael manages to maintain his friendship with Mina, as well as with his classmates. At the end of the novel, everyone is finally happy. The baby is named Joy.