This is the story of a civil war within the Civil War. Many mountain whites in Southern Appalachia opposed the Confederacy, especially when the South's conscription and impressment policies began to cause severe hardships. Deserters from the Rebel army hid in the mountains and formed guerrilla bands that terrorized unprotected Confederate homesteads. Violence escalated as Rebel guerrillas fought back. The conflict soon took on some of the ugliest aspects of class warfare between poorer mountain whites, who were usually Unionists, and the more well-to-do mountain property owners, who supported the Rebels. Mountain Partisans penetrates the shadowy world of Union and Confederate guerrillas, describes their leaders and bloody activities, and explains their effect on the Civil War and the culture of Appalachia.

Although it did not alter the outcome of the war, guerrilla conflict affected the way the war was fought. The Union army's experience with guerrilla warfare in the mountains influenced the North's adoption of hard war as a strategy used against the South in the last two years of the war and helped shape the army's attitude toward Southern civilians. Partisan warfare in Southern Appalachia left a legacy of self-imposed isolation and distrust of outsiders. Wartime hatreds contributed to a climate of feuds and extralegal vigilantism. The mountain economy never recovered from the war's devastating effects, laying the groundwork for the region's exploitation and impoverishment by outside corporations in the early 20th century.