Through them, the film explores several longstanding issues among the Navajo and their relations with the United States government and corporations: environmental racism, media and political representation, off-reservation adoption, and denial of reparations for environmental illnesses due to uranium mining in Monument Valley, Utah, which was unregulated for decades.

[2] The producers wanted to tell the full story of the Cly family, who were residents of the Navajo Nation in Monument Valley, Utah.

Through their story, the director and family intended to explore many of the issues with which the Navajo Nation has had to struggle since the early 20th century: land use and environmental contamination, off-reservation adoptions, health education, enforcement of treaty rights, relations with the United States government.

Much of the story in the 2000 film is told by the chief subject, Elsie Mae Cly Begay, the eldest of the children shown in The Navajo Boy.

Her mother Happy Cly died of lung cancer, which the family believed was caused by environmental contamination from unregulated uranium mining on the reservation.

[1] Elsie Mae's late grandparents, Happy and Willie Cly, were the main subjects of the earlier film.

[4] Elsie Mae Begay has become a public activist, telling her family and the Navajo Nation's story on college campuses and to Congress, to try to have practices changed and such health hazards controlled.

[3] In 2011, it was completing the first major project, to remove 20,000 cubic yards of materials from the abandoned Skyline Mine, near Begay's former home.