I wouldn't characterise Johnston's relationship with Clanton as a feud. Even is his earliest days as a cavalry leader prior to the Battle of Shiloh, General Bragg mentioned Clanton to another officer by saying, "Colonel Clanton is gallant to rashness." In other words, he had to be kept on a tight leash. Clanton resigned his commission soon afterwards, and then applied his energies to raising a "Legion" in South Alabama.

Clanton recruited during the winter and spring of 1863 among men who were still at home, so they might be regarded as reluctant warriors. Much like a politician on the campaign trail, Clanton made promises that he could not keep - that his troops would remain near home to guard the Florida border. By the summer of 1863 he had two regiments of infantry, two regiments of cavalry and two batteries, which won him a commission as brigadier general.

However, in late 1863 General Maury at Mobile got word of a Peace Society organized within Clanton's ranks. Some of his men planned to lay down their arms at Christmas and go home. They were arrested and brought to Mobile in chains, and a number of Clanton's officers were dismissed. The War Department thought it best to send Clanton's various units to other parts of the Confederacy. One of the infantry regiments was sent to Virginia and another to Dalton GA with one of the batteries. Clanton was allowed to keep the 6th Alabama Cavalry and his brother's battery, but was sent to the Tennessee Valley. He later made camp at Blue Mountain AL, near Oxford AL. The 7th Alabama Cavalry remained near Mobile, but was no longer under Clanton's command.

Capt Hardman, company commander of the 6th Alabama Cavalry, told a sad story in a letter written in May 1864. He and his regiment were stationed at the end of the rail line from central Alabama, and troops passed every day going to the Army of Tennessee. Meanwhile there were no orders for the 6th Alabama Cavary. Hardman confessed to his wife, he was almost ashamed to identify himself as a member of Clanton's command.

While at Blue Mountain Clanton devised a scheme to bring his 6th Alabama Cavalry to the Army of Tennessee. Adding it to the cavalry brigade which included his old 1st Alabama Cavalry, he could be placed in charge by virtue of seniority. Johnston evidently met Clanton and heard his plans. Clanton claimed that his command had been doing good service in Alabama by rounding up deserters and conscripts. Having no wish for Clanton to ruin one of his veteran brigades, General Johnston sent Clanton back to Alabama to continue his 'good service' there.

A few days later, Clanton's small command was routed at Ten Islands on the Coosa River. In his report General Sherman mentioned Clanton's cavalry, charitably describing it as a "very indifferent command" that Rousseau's raiders disposed of quite easily. Clanton lost badly in his only other action of the war at Bluff Spring FL, just over the Alabama line. Most of his men were driven into the swamps or captured at almost no loss to the Federal attackers. Clanton was badly wounded but survived the war.