Becky Morgan finally died on
July 21, 1861. In September,
Captain 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.
Morgan was promoted to
brigadier general (his highest rank) on
December 11, 1862. He received the thanks of the
Confederate Congress for his raids on the supply lines of
Union Maj. Gen. William Rosecrans in December and January, most notably his victory at the
Battle of Hartsville on
December 7. Also in December, 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.
Hoping to divert Union troops and resources in conjunction with the twin Confederate operations of
Vicksburg and the
Battle of Gettysburg in the summer of 1863, Morgan set off on the campaign that would become known as
the Great Raid of 1863 by Confederates, or derisively as the "Calico Raid" by Federals. Morgan crossed the Ohio River, and raided across southern Indiana and Ohio. After many skirmishes and battles, during which he captured and paroled thousands of Union soldiers, Morgan's raid almost ended on
July 19, 1863, at
Buffington Island, Ohio, when approximately 700 of his men were captured while trying to cross the
Ohio River into
West Virginia. (Intercepted by Union gunboats, less than 200 of his men succeeded in crossing.) Most of Morgan's men captured that day spent the rest of the war in the infamous
Camp Douglas Prisoner of War camp in
Chicago, which had a very high death rate. On
July 26, near
Salineville, Ohio, Morgan and his exhausted, hungry and saddlesore soldiers were finally forced to surrender.
On
November 27, Morgan and several of his officers, most notably
Thomas Hines, escaped from their cells in the
Ohio Penitentiary — the only successful escape from the prison in the 19th century — and returned safely to the South. Coincidentally, that same day his wife gave birth to a daughter, who died shortly afterwards before Morgan returned home.
Though Morgan's Raid was breathlessly followed by the Northern and Southern press and caused the Union leadership considerable concern, it is now regarded as little more than a showy but ultimately futile sidelight to the war. Furthermore, it was done in direct violation of his orders from Gen.
Braxton Bragg not to cross the river. Despite the Raiders' best efforts, Union forces had amassed nearly 110,000 Union militia in Illinois, Indiana and Ohio; dozens of
U.S. Navy gunboats along the
Ohio; and strong Federal cavalry forces, which doomed the raid from the beginning. The cost of the raid to the Federals was extensive, with claims for compensation still being filed against the U.S. government well into the early 20th century. However, the Confederacy's irreplaceable loss of some of the finest light cavalry in American history far outweighed the Union's replaceable losses in equipment and supplies. When taken in together with the defeats at Vicksburg and Gettysburg, the loss of Morgan's cavalry brigade dealt another serious blow to Confederate morale.
After his return from Ohio, Morgan was never again trusted by General Bragg. He was placed in command of Confederate forces in eastern Tennessee and southwestern
Virginia, but the men he was assigned were in no way comparable to those he had lost. Nevertheless, Morgan did what he could. On
September 4, 1864, he was surprised and killed while attempting to escape capture during a Union raid on
Greeneville, Tennessee. His men always believed that he had been murdered to prevent a second escape from prison, but it seems he was simply shot because he refused to halt.
Morgan was buried in
Lexington Cemetery. The burial was shortly before the birth of his second child, another daughter.