With the secession of Virginia in April 1861, Pemberton made his way to Washington, D.C. At the urging of his wife but against the remonstrances of his mother and brothers, he refused General Scott's offer of a colonel's commission, resigned, and cast his lot with Virginia. His rank changed quickly over the weeks that followed. On 28 April he became a lieutenant colonel in the Virginia state army. Ten days later he advanced to colonel in that service. On 15 June he was commissioned a major in the regular Confederate army and, two days later, brigadier general in the provisional Confederate army. His duties during this time and the months that followed consisted primarily of training and organizing cavalry and artillery and preparing the defenses of Norfolk and the James River. In November 1861 he was transferred to coastal South Carolina to assist department commander Robert E. Lee in the defense of that area. The following February, when Lee was recalled to Richmond, Pemberton succeeded to command of the Department of South Carolina, Georgia, and Florida and was promoted to major general in the provisional army. Southerners found it hard to overlook his northern birth, and Pemberton was anything but adept at public relations, even suggesting that, from an engineering standpoint, the emotionally significant Fort Sumter might as well be torn down. He was far from popular.
Steven E. Woodworth, "Pemberton, John Clifford," American National Biography Online, February 2000, http://www.anb.org/articles/05/05-00601.html.