The novel explores aspects of the lives of the Pillager, Puyat, and Kashpaw families on and near Ojibwe Native American reservations in the Dakotas. This novel focuses on Father Damien and the secret he keeps, as well as his relationships with other priests and nuns and with the members of his "flock," to whom he devotes his life.

Alternating between contemporary times and numerous past periods, the story gradually reveals the main secret concerning Father Damien's identity and misdeeds. Despite his efforts to lead a spiritual life and make amends, he is drawn into further secrecy.

From an introductory sequence presenting the priest's communication with the Pope, the novel moves back eighty years to tell the story of Sister Agnes and the challenges the young nun faces, often unsuccessfully. When she assumes the dead priest's identity, the stage is set for the long, complex saga that spans eight decades and keeps the reader wondering whether he/she will be exposed.

Secular characters and the hardships of Native life, including forced assimilation through boarding schools, are developed throughout. Sister Leopolda, formerly Pauline Puyat, ties this novel to Erdrich's earlier Tracks and helps hold the plot together through her attention to the "miracles" and the secrets she also harbors. Sent from the Vatican, Father Jude Miller investigates the miracles; by giving the reader knowledge of what Father Jude Miller may never discover, Erdrich makes us feel invested in the characters' lives and even complicit in helping them keep the past buried.