As the war progressed and the demand for additional troops grew, it became necessary to conscribe many who had failed to volunteer, and this became the occasion of fresh difficulty, as it always does. In the execution of the law enacted by the Confederate Congress relative to the tax in kind for the support of the army, Governor Shorter had to stem a current of popular opposition, and was held responsible by the masses for that which he did in compliance with the laws of congress. Added to all this was the necessity of the imposition of increased taxation for the support of the state government, and for the redemption of its bonds. In the prosecution of necessary tasks like these he became the victim of much popular wrath and unjust abuse. But duty was clear, and without wavering the breadth of a hair, or without chafing under the conditions, Governor Shorter met his obligations with steadiness and firmness. To have done less than he did would have made him recreant to his obligation, and everyone who did his duty at that time, and under conditions so stressful, fell under the same unreasonable public condemnation. A man of less nerve and less granite in his soul would have been swept off his feet in a public ordeal like this. On the expiration of his term, in 1863, he was a candidate for re-election, opposed by Thomas H. Watts, then attorney general of the Confederacy, and an opponent of Governor Shorter at the previous election. Public sentiment had grown so morbid during the tempestuous times of the former administration, that Governor Shorter failed of re-election. There was a burst of ungrateful expression of popular feeling, but the result was not unexpected. Governor Shorter had borne immense burdens in the face of popular clamor, and naturally and logically he preferred the indorsement of a people for whom he had done so much, while, on the other hand, it was a relief to be unburdened at the end of two years. After facing the odds, formidable and imposing, during the first two years of the struggle, and after resisting the inertia of popular discontent at every step, he retired from office with a stainless reputation, and, viewed at this distance, his course during the trying period of his administration is thoroughly vindicated, and in the galaxy of Alabama governors none has ever been more patriotic, none more firm in the prosecution of public duty, none calmer in a storm than John Gill Shorter. With the same serene temper with which he had deported himself in office, he retired to private life and resumed the practice of the law in the city of Eufaula.