In 1861, Stephens was elected as a delegate to the Georgia Secession Convention to decide Georgia's response to the election of Abraham Lincoln.
During the convention, as well as during the 1860 presidential campaign, Stephens, who came to be known as the sage of Liberty Hall, called for the South to remain loyal to the Union, likening it to a leaking but fixable boat.
During the convention he reminded his fellow delegates that Republicans were a minority in Congress (especially in the Senate) and, even with a Republican President, they would be forced to compromise just as the two sections had for decades.
Because the Supreme Court had voted 7–2 in the Dred Scott case, it would take decades of Senate-approved appointments to reverse it.
He voted against secession in the convention but asserted the right to secede if the federal government continued allowing northern states to nullify the Fugitive Slave Law with "personal liberty laws."
He was elected to the Confederate Congress and was chosen by the Congress as Vice President of the provisional government.
He took the provisional oath of office on February 11, 1861, then the 'full term' oath of office on February 22, 1862 (after being elected in November 1861) and served until his arrest on May 11, 1865.
Stephens officially served in office eight days longer than President Jefferson Davis; he took his oath seven days before Davis's inauguration and was captured the day after Davis.

On March 21, 1861, Stephens gave his famous Cornerstone Speech in Savannah, Georgia.
In it he declared that slavery was the natural condition of blacks and the foundation of the Confederacy.
He declared that, relative to the U.S. Constitution, "Our new Government is founded upon exactly the opposite ideas; its foundations are laid, its cornerstone rests, upon the great truth that the negro is not equal to the white man; that slavery, subordination to the superior race, is his natural and normal condition."

In 1862, Stephens first publicly expressed his opposition to the Davis administration.
Throughout the war he denounced many of the president's policies, including conscription, suspension of the writ of habeas corpus, impressment, various financial and taxation policies, and Davis's military strategy.

In mid-1863, Davis dispatched Stephens on a fruitless mission to Washington, D.C. to discuss prisoner exchanges, but the Union victory of Gettysburg made the Lincoln Administration refuse to receive him.
As the war continued and the fortunes of the Confederacy sank lower, Stephens became more outspoken in his opposition to the administration.
On March 16, 1864, Stephens delivered a speech to the Georgia Legislature that was widely reported in both the North and the South.
In it, he excoriated the Davis Administration for its support of conscription and suspension of habeas corpus, and supported a block of resolutions aimed at securing peace.
From then until the end of the war, as he continued to press for actions aimed at bringing about peace, his relations with Davis, never warm to begin with, turned completely sour.

On February 3, 1865, Stephens was one of three Confederate commissioners who met with Lincoln on the steamer River Queen at the Hampton Roads Conference, a fruitless effort to discuss measures to bring an end to the fight.
Stephens and Lincoln had been close friends and Whig political allies in the 1840s.
Although peace terms were not reached, Lincoln did agree to look into the whereabouts of Stephens's nephew, Confederate Lieutenant John A. Stephens.
When Lincoln returned to Washington, he ordered the release of Lieutenant Stephens.

Stephens was arrested for treason against the United States at his home in Crawfordville, on May 11, 1865.
He was imprisoned in Fort Warren, Boston Harbor, for five months until October 1865.
In 1861, Stephens was elected as a delegate to the Georgia Secession Convention to decide Georgia's response to the election of Abraham Lincoln. During the convention, as well as during the 1860 presidential campaign, Stephens, who came to be known as the sage of Liberty Hall, called for the South to remain loyal to the Union, likening it to a leaking but fixable boat. During the convention he reminded his fellow delegates that Republicans were a minority in Congress (especially in the Senate) and, even with a Republican President, they would be forced to compromise just as the two sections had for decades. Because the Supreme Court had voted 7–2 in the Dred Scott case, it would take decades of Senate-approved appointments to reverse it. He voted against secession in the convention but asserted the right to secede if the federal government continued allowing northern states to nullify the Fugitive Slave Law with "personal liberty laws." He was elected to the Confederate Congress and was chosen by the Congress as Vice President of the provisional government. He took the provisional oath of office on February 11, 1861, then the 'full term' oath of office on February 22, 1862 (after being elected in November 1861) and served until his arrest on May 11, 1865. Stephens officially served in office eight days longer than President Jefferson Davis; he took his oath seven days before Davis's inauguration and was captured the day after Davis.
On March 21, 1861, Stephens gave his famous Cornerstone Speech in Savannah, Georgia. In it he declared that slavery was the natural condition of blacks and the foundation of the Confederacy. He declared that, relative to the U.S. Constitution, "Our new Government is founded upon exactly the opposite ideas; its foundations are laid, its cornerstone rests, upon the great truth that the negro is not equal to the white man; that slavery, subordination to the superior race, is his natural and normal condition."
In 1862, Stephens first publicly expressed his opposition to the Davis administration. Throughout the war he denounced many of the president's policies, including conscription, suspension of the writ of habeas corpus, impressment, various financial and taxation policies, and Davis's military strategy.
In mid-1863, Davis dispatched Stephens on a fruitless mission to Washington, D.C. to discuss prisoner exchanges, but the Union victory of Gettysburg made the Lincoln Administration refuse to receive him. As the war continued and the fortunes of the Confederacy sank lower, Stephens became more outspoken in his opposition to the administration. On March 16, 1864, Stephens delivered a speech to the Georgia Legislature that was widely reported in both the North and the South. In it, he excoriated the Davis Administration for its support of conscription and suspension of habeas corpus, and supported a block of resolutions aimed at securing peace. From then until the end of the war, as he continued to press for actions aimed at bringing about peace, his relations with Davis, never warm to begin with, turned completely sour.
On February 3, 1865, Stephens was one of three Confederate commissioners who met with Lincoln on the steamer River Queen at the Hampton Roads Conference, a fruitless effort to discuss measures to bring an end to the fight. Stephens and Lincoln had been close friends and Whig political allies in the 1840s. Although peace terms were not reached, Lincoln did agree to look into the whereabouts of Stephens's nephew, Confederate Lieutenant John A. Stephens. When Lincoln returned to Washington, he ordered the release of Lieutenant Stephens.
Stephens was arrested for treason against the United States at his home in Crawfordville, on May 11, 1865. He was imprisoned in Fort Warren, Boston Harbor, for five months until October 1865.
Alexander H. Stephens