The only friend Emmie Hatton has ever had at the Craven Home for Orphaned Children is Lucy, the little black kitten that visits her on the fire escape every day. But when the children of Craven Home are evacuated out of London because of the war, heartbroken Emmie is forced to leave sweet Lucy behind. The children are sent to Misselthwaite Manor, a countryside mansion full of countless dusty rooms and a kind, if busy, staff. Emmie even finds a gruff gardener and an inquisitive little robin that just might become new friends.

But soon, in the cold, candle-lit nights at Misselthwaite, Emmie starts discovering the secrets of the house—a boy crying at night, a diary written by a girl named Mary, and a very secret, special garden.