On the heels of the turbulent "Bleeding Kansas" era which swept this region in the late 1850s lingered the shadow of civil war. In April of 1861, war between the Union and Confederacy was officially declared. The old frontier military post of Fort Scott had been abandoned for over eight years and a town of the same name had grown in its place. With the advent of war, the U.S. Army returned and established a military headquarters in the town of Fort Scott.

As early as August of 1861, the Union Army occupied its former frontier hospital, the adjacent barracks and stables, and began construction on new warehouses, powder magazines, wells, a blacksmith shop, an icehouse, a military prison, and over 40 miles of fortifications around Fort Scott. As the site of a quartermaster supply depot and countless regimental camps, Fort Scott would become the largest and strongest Union point south of Fort Leavenworth.