A Southern Unionist, he fought for the Union Army during the American Civil War, commanding units at Mill Springs, Stones River, Chickamauga, Franklin, Nashville, Bentonville, and in the Knoxville and Atlanta campaigns.

He and his parents moved to Campbell County, Tennessee, the following year, where they settled on a farm along Cove Creek, 5 miles (8.0 km) south of Jacksboro.

Nelson that called for violent measures to be taken if the Convention's demands were not met, but gradually came to favor a more moderate set of resolutions offered by Knoxville attorney Oliver Perry Temple.

[6] While in Greeneville, Cooper made a secret pact with several other East Tennessee Convention delegates, including Richard M. Edwards and Robert K. Byrd, to return to their respective homes and begin recruiting and drilling men to defend the region against a Confederate invasion.

[5][8] In March of the same year, Cooper's company attacked and broke through Confederate defenses at Big Creek Gap, a key mountain pass in northern Campbell County.

In July 1862, Cooper and his regiment attacked a Confederate force at Wallace's Crossroads (near modern Andersonville, Tennessee), killing five soldiers and capturing several others.

[9] Cooper skirmished with Confederate forces on Lookout Mountain during the latter phases of the Battle of Chickamauga in September 1863, and took part in the Knoxville Campaign in late 1863 and early 1864.

[9] Upon reaching the front, he helped thwart Hood's assault on the city, charging and capturing two artillery pieces and a number of Confederate soldiers.

Though he placed second, ahead of fellow Union officer Robert K. Byrd and future congressman Leonidas C. Houk, he was still well behind the winner, Horace Maynard.

[16] Brownlow's hardline stance toward former Confederates created widespread unrest among Rebel vigilante groups across the state, most notably the Ku Klux Klan.

[17] Cooper quickly formalized the Guard's structure, dividing its 1,900 recruits into two regiments, each containing an equal number of companies from each of the state's three grand divisions.

[22] Toward the end of his gubernatorial tenure in January 1869, Brownlow, citing another rise in Klan violence, reactivated the State Guard, and reappointed Cooper its commander.

Cooper declared that any Klansmen captured would be hanged, and warned local authorities in non-affected counties that martial law would be imposed on them, as well, if they did not aid in the fight against the Klan.

[23] In late February 1869, however, Brownlow's successor, Dewitt Clinton Senter, softened the martial law decree, and afterward began demobilizing the Guard.

[25] Historians in the late 19th century were often critical of the State Guard, describing it as an instrument of oppression, and going so far as to compare it to Oliver Cromwell's New Model Army of 17th-century England.

"[26] He suggests that in spite of sporadic reports of drunkenness and violence, the Guard was unusually well-behaved, and cites Cooper's leadership and emphasis on discipline as the reason for this.

When Alfred Cate, Roderick R. Butler, and Thomas H. Pearne scuffled over the chairman's gavel, a frustrated Cooper restored control and convinced the delegates to adjourn for the day in order to cool off.

[31] Shortly after his arrival in Stafford County, he was appointed moderator of the South Central Baptist Association of Kansas, a position he held until 1909.