In Tokyo, Japan, college student Hana falls in love with a werewolf and has two half-werewolf children with him: a daughter, Yuki, and a year later a son, Ame. Soon after, their father is killed in an accident while hunting food for the children.
Hana's life as a single mother is difficult; Yuki and Ame constantly switch between their human and wolf forms, and Hana has to hide them from the world. When she is visited by social workers concerned that the children have not had vaccinations, Hana moves the family to the countryside away from prying neighbors. She works hard to repair a dilapidated house and sustain the family on their own crops.
One winter day, Ame almost drowns in a river after trying to hunt a Kingfisher, but Yuki rescues him and Ame becomes more confident. Yuki begs her mother to let her go to school like other children. Hana accepts on the condition that Yuki keeps her wolf nature secret. Though Yuki's classmates find her strange at first, she soon makes friends. However, Ame is more interested in the forest and takes lessons from an elderly fox about survival in the wild.
In fourth grade, Yuki's class receives a new transfer student, Souhei, who realizes something is strange about her. When he pursues her, Yuki transforms into a wolf and inadvertently injures him, leading to a meeting with their parents and teachers. Souhei tells them a wolf attacked him, absolving Yuki of the blame. The two become friends.
Later, Yuki and Ame disagree over whether they are human or wolf. Two years later, while Yuki is at school, a storm gathers and Ame disappears into the forest to help his fox teacher; Hana follows him. The other children are picked up from school by their parents, leaving Yuki and Souhei alone. Yuki shows Souhei that she can transform into a wolf; he promises to keep her secret and tells her that he already knew her secret.