Daniel's Return tells the story of a Hopi Indian boy who is forced to leave his family and friends on the Hopi Indian Reservation in Arizona to attend compulsory Bureau of Indian Affairs schools that at the time (the 1950s) separated Native American children from their tribal cultures in an effort to assimilate them into the dominant Anglo culture. At school he is taught that his race is inferior, his religion is evil and his way of life is primitive and that only by adopting the culture, religion and values of white society will he ever make something of himself.

Daniel's father died before his son was born, so for Daniel growing up without a father is made doubly difficult by being torn away from his mother, his uncle and his whole way of life. He runs away from every school he is sent to until the government authorities decide to send him to a school so far from his family that he will never be able to find his way home again. But in this they are wrong because Daniel, in running away from this last school, is also running away from an abusive army colonel who tries to exploit Daniel's innocence for his own twisted purposes. In the end Daniel successfully escapes from his new school, his powerful abuser and a system designed to uproot Native American children from their homes and annihilate their identity.

The narrative is rich in Hopi myth, legend and history and takes place against the backdrop of postwar America when nuclear testing in the deserts of the American Southwest was routine and the Enforced Assimilation Era in Native American history was in full swing.