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At the outbreak of the civil was he joined the Kansas Legion in Washington D.C. This put him in a good location to gain attention, and he was soon promoted to lieutenant of cavalry for successfully carrying dispatches from Washington to General Scott.
From Washington he was sent west. He was present at the battle of Shiloh, receiving a promotion to brevet first lieutenant. After Shiloh he was part of Buell’s army sent east to capture Chattanooga. When Braxton Bragg responded with his invasion of Kentucky, Buell (and McCook) followed. McCook was promoted to captain for his conduct at the battle of Perryville.
Buell was soon replaced by Rosecrans. His successful advance to Chattanooga met with disaster soon afterwards at Chickamauga. Once again McCook was promoted for his conduct in the battle, this time to major. He was promoted to lieutenant-colonel as a result of his cavalry operations in East Tennessee in the aftermath of the siege of Chattanooga. Finally, on 27 April 1864 he was promoted to brigadier-general of volunteers, and appointed to command the cavalry in the Army of the Cumberland.
This meant that he played a prominent role in Sherman’s march to Atlanta. The cavalry came especially to the fore once Sherman had reached Atlanta. Sherman hoped to use his cavalry to reach behind the Confederate lines and cut off their supplies. A first attempt at the end of July 1864 failed. McCook had been sent out with 3,000 men as part of a two pronged attack that had as an additional target the liberation of the Andersonville prisoner of war camp. McCook’s raid was repelled with 950 losses, but at least he did not suffer the fate of Major-General George Stoneman, who was himself captured.
After the fall of Atlanta, Sherman split his forces. General Thomas, with the Army of the Cumberland, returned north to Tennessee to deal with the remaining Confederate forces under General Hood. McCook was sent into western Kentucky and missed Hood’s invasion.
McCook’s final military service came in Wilson’s raid through Alabama and Georgia in the spring of 1865. McCook commanded the first division in Major-General James H. Wilson’s army during this final raid of the war. On 20 April the expedition received news of the truce between Sherman and General Johnston. McCook was detached with a force of 500 men and sent to Tallahassee, to accept the surrender of Florida.
He remained in Florida, as military governor, until June 1865. He was promoted to brevet brigadier-general of regulars and brevet major-general of volunteers as a reward for his wartime service. He remained in public service for another decade, first as United States minister to Hawaii (to 1869), and then as Governor of Colorado (not an elected post, but one in the gift of President U. S. Grant). He was not popular in Colorado, and only served one full term and part of a second term, resigning early in 1875. McCook went on to have a very successful career in business, initially in Colorado and the west, but also in Mexico. He was also an early investor in the new telephone industry.