Stanton was politically opposed to
Republican Abraham Lincoln in
1860. After Lincoln was elected president, Stanton agreed to work as a legal adviser to the inefficient Secretary of War,
Simon Cameron, whom he replaced on
January 15, 1862. He accepted the position only to "help save the country." He was very effective in administering the huge War Department, but devoted considerable amounts of his energy to the persecution of Union officers whom he suspected of having traitorous sympathies for the South. On August 8, 1862 Stanton issued an order to "arrest and imprison any person or persons who may be engaged, by act, speech or writing, in discouraging volunteer enlistments, or in any way giving aid and comfort to the enemy, or in any other disloyal practice against the United States."
The president recognized Stanton's ability, but whenever necessary Lincoln managed to "plow around him." Stanton once tried to fire the Chief of the War Department Telegraph Office,
Thomas Eckert. Lincoln prevented this by defending Eckert and told Stanton he was doing a good job. This led to Eckert keeping his job. Yet, when pressure was exerted to remove the unpopular secretary from office, Lincoln replied, "If you will find another secretary of war like him, I will gladly appoint him." Stanton became a Republican and apparently changed his opinion of Lincoln. At Lincoln's death Stanton remarked, "Now he belongs to the ages," and lamented, "There lies the most perfect ruler of men the world has ever seen." He vigorously pursued the apprehension and prosecution of the conspirators involved in Lincoln's assassination. These proceedings were not handled by the civil courts, but by a
military tribunal, and therefore under Stanton's tutelage. Stanton has subsequently been accused of
witness tampering, most notably of
Louis J. Weichmann, and of other activities that skewed the outcome of the trials.