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From April 1865 until September 1866, Sprague was the assistant commissioner of the Freedmen's Bureau for the district of Arkansas, serving under Maj. Gen. Oliver O. Howard. He was in charge of operations in Missouri, Kansas, and subsequently the Indian Territory. In September 1865, he declined a lieutenant-colonelcy in the Regular Army and mustered out of the service. He was succeeded by Edward O. C. Ord.