American Civil War
Like most Kentuckians, Morgan did not initially support declaring secession from the United States. Immediately after Lincoln's election in November 1860, he wrote to his brother, Thomas Hunt Morgan, then a student at Kenyon College in northern Ohio, "Our State will not I hope secede I have no doubt but Lincoln will make a good President, at least we ought to give him a fair trial & then if he commits some overt act all the South will be a unit." By the following spring, Tom Morgan (who also had opposed Kentucky's secession) transferred home to the Kentucky Military Institute and began to support the Confederacy. Just before the Fourth of July, by way of a steamer from Louisville, he quietly left for Camp Boone, just across the Tennessee border, to enlist in the Kentucky State Guard. John stayed home in Lexington to tend to his troubled business and ailing wife. Becky Morgan died on July 21, 1861.
In September, Morgan and his militia company went to Tennessee and joined the Confederate States Army. Morgan soon raised the 2nd Kentucky Cavalry Regiment and became its colonel on April 4, 1862.
Morgan and his regiment fought at the Battle of Shiloh in April 1862, and he soon became a symbol to secessionists, in their hopes of occupying Kentucky for the Confederacy. A Louisiana writer, Robert D. Patrick, compared Morgan to Francis Marion and wrote that "a few thousands of such men as his would regain us Kentucky and Tennessee."
In his first Kentucky raid, Morgan left Knoxville on July 4, 1862, with almost 900 men and, in three weeks, swept through Kentucky, deep in the rear of Major General Don Carlos Buell's army. He reported the capture of 1,200 U.S. soldiers, whom he paroled, acquired several hundred horses, and destroyed massive quantities of supplies. He unnerved Kentucky's U.S. military government and President Abraham Lincoln received so many frantic appeals for help that he complained that "they are having a stampede in Kentucky." Historian Kenneth W. Noe wrote that Morgan's feat "in many ways surpassed J. E. B. Stuart's celebrated 'Ride around McClellan' and the Army of the Potomac the previous spring." The success of Morgan's raid was one of the key reasons that the Confederate Heartland Offensive of Braxton Bragg and Edmund Kirby Smith was launched that fall, assuming that tens of thousands of Kentuckians would enlist in the Confederate Army if they invaded the state.
As a colonel, the widow of Brigadier General Barnard Elliott Bee Jr. presented him with a Palmetto Armory pistol. The Museum of the American Civil War now owns that pistol.
Following the Battle of Perryville, both armies returned to Tennessee, to regroup before the ensuing Stones River Campaign. Morgan's cavalry was active during this period, launching multiple raids and strikes on the supply lines feeding Maj. Gen. William S. Rosecrans' Union army at Nashville. Their surprise attack on Hartsville on December 7, scored notable victory.
Morgan was promoted to brigadier general (his highest rank) on December 11, 1862, though Jefferson Davis did not sign the Promotion Orders until December 14, 1862.
On December 14, 1862, Morgan married Martha "Mattie" Ready, the daughter of Tennessee United States Representative Charles Ready and a cousin of William T. Haskell, another former U.S. representative from Tennessee.
From December 22, 1862, to January 5, 1863, Morgan's cavalry brigade made a 500-mile Christmas Raid into central Kentucky. While Morgan's men were away on this raid, the two main armies fought the Battle of Stones River.
Morgan would receive the thanks of the Confederate Congress on May 1, 1863, for these raids.
