Pinckney helped form and then lead the St James Mounted Riflemen whose purpose was to defend the various plantations on the Santee River delta from Northern raids. He further used his land at Echaw Plantation to build Battery Warren to protect a Confederate railroad bridge over the Santee. Over time he and his men were re-organized under the command of then-Major Arthur Middleton Manigualt in McClellanville and then, later, under General M. C. Butler they were sent to Virginia. At the Battle of Haw's Shop Pinckney was captured. As a prisoner-of-war, he was nearly starved to death and held in the line of fire at Morris Island by Union soldiers in retaliation for the treatment of Union soldiers held by the Confederacy. He and the others so treated became known in the Confederacy as the Immortal Six Hundred for their refusal to take an oath of allegiance to the United States. Eventually, Pinckney was exchanged for Union soldiers and paroled.