Stephens continued to argue against secession during the lead-up to the Civil War. Despite these misgivings, he was chosen to be the first vice president of the Confederate States of America during the Confederate Congress in February 1861. For many in the Confederacy, Stephens’ reputation as a moderate and a unionist—albeit a strong supporter of slavery—was seen as a valuable tool in winning border states over to the Southern cause.
After taking office Stephens played an influential role in drafting the Confederacy’s new constitution. He then introduced the new government during a stump speech in Savannah on March 21, 1861. In what became known as the “Cornerstone Speech,” Stephens argued that the new Confederate government was based upon “the great truth that the negro is not equal to the white man.”
After the beginning of the Civil War in April 1861, Stephens moved to the new Confederate capital in Richmond, Virginia, and took part in administrative preparations for the war effort. During this time he repeatedly advocated that the Confederacy delay large-scale military action in order to properly plan and equip itself for prolonged war. Stephens was unenthusiastic about his position as vice president, which granted him little power and largely relegated him to the role of passive observer over the Confederate Congress. Nevertheless, he was reelected to his post in February 1862 after his one-year provisional appointment expired.
Starting in 1862 Stephens began the first of many arguments with President Jefferson Davis over the management of the war effort. A staunch proponent of limited government, Stephens took issue with Davis’s suspension of habeas corpus, which allowed arrests without charge. In September 1862 he published an unsigned letter in a Georgia newspaper condemning the policy of conscription, which gave the Confederate government the power to draft troops ahead of their state militias. He would later clash with Davis over both impressment and the Confederate combat strategy. Disillusioned with Davis’ policies and feeling unneeded, Stephens regularly left the Confederate capital to spend extended periods away at his home in Georgia.
In July 1863 Stephens was sent to Washington, D.C., on a mission to discuss prisoner exchanges with the Union. Anxious to end the war, Stephens also hoped to broach the subject of reaching a peace agreement. His journey only took him as far as Newport News, Virginia, where—following the crucial Union victory at the Battle of Gettysburg—he was informed that the U.S. government would not consider opening negotiations with him.
Stephens next redoubled his efforts to oppose Davis, who he believed had become too powerful. In March 1864 he gave a speech to the Georgia state legislature outlining his criticisms of Davis, and was denounced by many Southerners as a traitor. His opposition to Davis became so pronounced that in late 1864 he received a letter from Union General William T. Sherman—then undertaking his “March to the Sea”—encouraging Stephens to meet and discuss the possibility of Georgia forming an independent peace agreement with the Union. Stephens refused the invitation, but his relationship with Davis remained strained for the rest of the war.
Stephens maintained his states’ rights philosophy into 1865, when he made another failed attempt to negotiate peace with the U.S. government. He then returned to his home in Georgia, where he was arrested on May 11, 1865. He was imprisoned in Fort Warren, Boston Harbor, for five months before being pardoned by President Andrew Johnson in October 1865.