His ability established on that occasion led to his becoming an elector in the approaching presidential contest in behalf of Breckenridge and Lane. An elector for the state at large, he canvassed Alabama throughout, and came to be known first, as an orator of great resource and power. This, in turn, led to his choice as a member of the secession convention of Alabama. When the war began, he became major of the Fifth Alabama Regiment, and on the reorganization of the regiment, was chosen lieutenant colonel of that command. Authorized by the war department to raise a cavalry regiment, he returned to Alabama and did so. Going with his new regiment to the western army, he was later assigned to the headship of the conscript bureau in Alabama, according to the request of the Alabama delegation in congress. Later still, he was notified by General R. E. Lee that he had been made a brigadier general and assigned to the command of Rode's old brigade. While on his way to the Virginia front, he learned in Richmond of the death of Colonel Webb, who had been associated with him in raising the cavalry regiment, and that he (Morgan) had been elected again to the colonelcy of the regiment. On learning this, he declined the offered promotion in the Army of Northern Virginia, and returned. He was again made a brigadier general, and toward the close of the war was in the command of a division in the Tennessee army. During the period of the reconstruction, General Morgan became the most sturdy and famous champion of the people of Alabama, and greatly endeared himself to them by his incessant labor in resisting the encroachments on their rights. When, at last the power of reconstruction was broken, he was, in 1876, elected to the national senate to succeed the notorious George E. Spencer. From that time till his death, he was the political idol of the Democratic party in the state of Alabama. For full thirty years he served with distinguished ability in the senate, and died in the harness of a statesman.