On March 8, 1862, the Cooper caravan reached Elkhorn Tavern, Benton County, Arkansas. The Battle of Pea Ridge opened that day and the Major’s party was caught in the midst of it. The Major joined the Cherokee Brigade of the Confederate Army and ordered the slaves to butcher the steers for meat. Early in the battle this veteran officer received a wound and was carried from the field. Dr. Alvah Jackson had set up a crude hospital near the Indian Healing spring twenty miles to the east and the Major reported there for treatment. After a few weeks he was dismissed and returned to his command.
Major Cooper returned to Dr. Jackson for treatment in 1863, but was soon released. His last visit, near the end of the war, is reported by L. J. Kalklosch as follows:
“It was in February, 1865, and the ‘Yankees’ were numerous in the country, so that the ‘Johnnies’ were compelled to make themselves scarce or fall into the hands and care of the enemy. Major Cooper did not care to have ‘Uncle Sam’ issue rations to him, so he, with four of his men, were piloted to a secret cave, (the Old Rock House shelter) by his medical advisor (Dr. Alvah Jackson), near the now famous Basin Spring, and visitors find it one of the objects of interest during their rambles over the city. Here he remained for about two months and used freely of the healing waters. But eventually their secret hiding place was discovered by the ‘Boys in Blue’ and they thought it best to find different quarters. The conclusion was not reached, nor steps taken too soon as they narrowly escaped being captured by the Federals. One beautiful feature in the Major’s escape was that he was fully able to meet the emergency as the water had fully relieved him of all his troubles.”[9]
As the war neared its close, the Major bought a tract of land bordering the present City of Eureka Springs on the west. He secured fresh oxen and drove to St. Louis to get saw mill equipment. He built his mill in “Cooper Hollow” and constructed a log house for his home. At the end of the war his slaves were freed, but he succeeded in getting white labor that had been “fired” from Mrs. Massman’s saw mill on Leatherwood Creek. For several years he operated this mill, hauling the lumber to market at Pierce City, Missouri.