In a remote monastery in 1940s Australia, a mission for Aboriginal children is run by a renegade nun, Sister Eileen (Cate Blanchett). A new charge (Aswan Reid) is delivered in the dead of night a boy who appears to have special powers. When the monastery takes possession of a precious relic, a large carving of Christ on the cross, the new boy encounters Jesus for the first time and is transfixed. However, the boys Indigenous spiritual life does not gel with the missions Christianity and his mysterious power becomes a threat. Sister Eileen is faced with a choice between the traditions of her faith and the truth embodied in the boy, in this story of spiritual struggle and the cost of survival.