Following the outbreak of the Civil War, Paine was elected
colonel of the
9th Illinois Infantry. In September 1861, he was appointed as a
brigadier general of volunteers. He commanded a brigade at
Paducah, Kentucky, a critical supply depot for the Federal army. There, Paine developed a reputation for harshness and cruelty toward the civilian populace. He ordered all
guerrilla fighters caught within his territory to be executed. Paine commanded the 4th Division of the
Army of the Mississippi at the
Battle of New Madrid and
Island Number Ten in
Missouri while leading the 1st Division. He also served in the
Siege of Corinth under
William S. Rosecrans. He subsequently headed the District of West Kentucky, where his men were deployed guarding railroads from
Confederate raiders from November 1862 until April 1864. His headquarters were in
Gallatin, the seat of Sumner County in
Middle Tennessee. It was a center of regional railroads. Tennessee was occupied by Union troops from 1862 into 1870. His son Phelps Paine was a
captain in the Union Army and also assigned to Gallatin. Paine, who was in command in heavily secessionist areas of Kentucky and Tennessee, was charged by some citizens with repressing and stealing from them. In addition to publicly executing suspected spies in the Gallatin town square, he was accused of what was called "chasing the fox with fresh horses"—having his men chase down and kill prisoners after they had been set free on old horses. On April 29, 1864,
Maj. Gen. William T. Sherman reassigned Paine and a
regiment of his infantry to a post in
Tullahoma, Tennessee, to guard bridges crossing the
Duck and
Elk rivers. Paine later commanded the military District of Illinois, but he resigned in November 1864 and was replaced by
John Cook. A special military commission investigating Paine's actions in Kentucky and Tennessee found him guilty on several counts, including corruption, extortion, unjust taxation, fencing stolen goods, sending innocent civilians to Canada, and immorality. Several modern historians have questioned the accuracy of the findings of this commission, as the investigators were aligned with the Union Democrats (pro-union, pro-slavery). But several of Paine's defenders were Unconditional Unionists (pro-union, anti-slavery). At this time the Purchase area of western Kentucky (where Paducah is located) was the only area of the Bluegrass State that was overwhelmingly pro-secession. Confederate cavalry and guerillas operated with impunity in much of the Purchase, and Paine believed he needed strict military rule to keep control. Later Paine was subject to a full
court martial on essentially the same charges. He was acquitted on all but a charge of cursing a superior officer. His punishment was to be reprimanded by the president of the United States in general orders.
Secretary of War Edwin Stanton refused to enforce the sentence. According to Kentucky historian Berry Craig, "In the last analysis evidence is strong that the local animus toward Paine, perpetuated by nineteenth and twenty century historians, was rooted in his strongly held abolitionist views, in his support for the enlistments of African Americans into the Union forces and in his belief in black equality with whites." Paine resigned from the Army in April 1865. ==Postwar years==