Ten-year-old Michael and his family move to a dilapidated house. On top of feeling uprooted and haunted by thoughts of the house’s previous owner, Ernie Myers, Michael’s baby sister has a life-threatening heart condition, and so a scary doctor whom Michael calls Doctor Death visits her often.
While his mum and dad are preoccupied fixing the house and taking the baby to the hospital, Michael is left to entertain and comfort himself. One day, Michael discovers a strange, sickly creature in the collapsing garage. The creature does not explain who he is or what ails him, but he allows Michael to feed him Chinese Food and aspirin. The creature’s poor health adds to Michael’s worries, but Michael doesn’t tell anyone, as he’s afraid the creature is a figment of his imagination.
Michael goes to school, but he’s too worried to play football during recess with his friends. Meanwhile, he meets and befriends Mina, a girl his age who lives next door and whose mother, Mrs. McKee, homeschools her. Mina introduces Michael to art, poetry, evolution, and the remarkable nature of birds. Through Mina, Michael becomes more curious and imaginative; he wonders about the similarity he has noticed between the sickly creature’s shoulder blades and wings.
The baby’s health worsens, and Mum takes her to stay at the hospital. Michael has a fit of nervous trembling and can’t attend school. One day while Dad and Michael visit the baby in the hospital, Michael asks Doctor MacNabola how to care for a person with arthritis (which he speculates the creature has).
Later, Mina shows Michael a secret place: an old house her grandfather left to her where owls are nesting in the attic. Emboldened by Mina’s trust in him, Michael decides to show Mina the creature in the garage. Michael and Mina decide to move the creature to the owl house where he will be safer. After they make him comfortable there, the creature says his name is Skellig. Michael and Mina sneak out the next few nights to visit Skellig, who has since crawled from the first to the third floor of the house.
A few days later, Michael’s friends Leaky and Coot come over to play. They tease Michael for hanging out with Mina. Hurt by this, Mina fights with Michael. That night, however, Michael and Mina meet as usual, signaling each other with their owl call. After making up, they go to see Skellig, who is in the attic eating dead animals the owls left on the windowsill. Skellig, Michael, and Mina dance. Then shadowy wings sprout from their shoulders, and they rise off the ground.
Dad catches Michael out one night and fears that he is sleepwalking. At Doctor Death’s suggestion, Michael goes back to school. A few days later, the baby goes in for heart surgery. While Dad and Mum attend the surgery, Michael goes to Mina’s; he focuses on listening to the baby’s heartbeat within his own heartbeat, hoping to protect the baby from afar. Michael and Mina go to see Skellig, but they can’t find him, and then Michael passes out. When he comes to, he fears that he can’t feel the baby’s heartbeat any longer and laments that Skellig is gone.
Miraculously, the baby’s surgery goes well, and Michael joins Mum and Dad at the hospital. Mum tells Michael the story of a vision she had the night before the surgery: a strange, dirty creature came to the room and picked up the baby; at first, Mum was scared, but then she knew everything would be alright. Later that night, Michael and Mina go back to the owl house. Skellig flies through the window. He thanks Michael and Mina for saving his life and then flies away again, this time for good.
The baby continues to recover from surgery, and Michael’s football skills improve at school. Dad has builders come to knock down the garage, and he and Michael make plans for the new spacious yard. Mum comes home with the baby. Mina comes over and meets the baby. She gifts the family a painting she made of Skellig. After Mina leaves (Michael swearing he can see the shadowy wings on her shoulders) the family decide to name the baby Joy.