Lee continued his work in Washington, living at his wife's ancestral home at Arlington. In 1861, the South did secede and Virginia soon followed. Lee was offered a command in the Union Army but declined to accept the assignment because of his oath, loyalty, and ancestry to Virginia. It was a difficult decision for Lee, but his "allegiance was to Virginia" and his strong family roots to Virginia. With some regrets, Lee resigned his commission and moved his family to Richmond; never to see the home at Arlington again (Robert E. Lee's Resignation Letter). Lee offered his services to the state of Virginia and was placed in command of all military forces from that state. He was later assigned as "personal military advisor to President Jefferson Davis," which was a very difficult job. Lee had to coordinate numerous operations involving officers who were very sensitive about their command positions and obligations. It was a difficult time, and Lee suffered the brunt of heavy criticism.

In the spring of 1862, the Union Army of the Potomac, commanded by General George McClellan, was poised to strike the city of Richmond. In a pitched battle at Seven Pines, General Joseph Johnston, commanding the Confederate forces, was seriously wounded. Lee was immediately assigned to replace Johnston and he took command of the army, which he renamed the Army of Northern Virginia. Despite some early difficulties, General Lee undertook the new assignment with vigor and spirit. Directing his troops near Richmond with those of General "Stonewall" Jackson in the Shenandoah Valley, Lee met the Union threat on two fronts. After quickly smashing the Union forces in the Valley, General Jackson rushed his troops to Richmond and joined General James Longstreet's Corps in attacking McClellan's army. Together, Lee and his officers were able to rout the Union threat during the Seven Days Battles.

"He has lost his left arm; but I have lost my right arm." —General Robert E. Lee referring to General "Stonewall" Jackson

What followed was a set of victories against seemingly insurmountable odds. General Lee's army was always outnumbered, out gunned, and often in a poor position to attack or defend. General Lee, however, was a practical strategist with an engineer's sense, who was willing to take risks to outmaneuver his opponents. The support of excellent commanders contributed to repeated victories against the Union Army. Lee suffered several setbacks during the Maryland Campaign in 1862, which resulted in the Battle of Antietam. Still, General Lee's thin line held most of the battlefield at the end of America's bloodiest single-day of fighting, giving him a strategic victory. (Photograph to the right: Mathew Brady portrait of Lee in 1865.) Subsequently, he was forced to retreat across the Potomac River and back to Virginia. After the Battle of Fredericksburg in December, Lee spent the winter rebuilding his battered army. The Union Army also rebuilt itself and opened the spring of 1863 with a surprise move against Lee's forces. The Battle of Chancellorsville, Virginia, (one of Lee's greatest victories) was at a very high cost when "Stonewall" Jackson, his most trusted officer, was mortally wounded. Despite the loss of his beloved corps commander, Lee continued and invaded the North again. His troops successfully marched through Maryland and southern Pennsylvania until they clashed with Union forces at Gettysburg. The Battle of Gettysburg was a costly defeat for the Army of Northern Virginia; Lee felt a great and personal responsibility for the loss. Lee even offered his resignation, but the Confederate government displayed great confidence in the commander and refused his resignation.

General Lee faced a new antagonist in the spring of 1864. After a succession of Union victories in Tennessee and Mississippi, General Ulysses S. Grant arrived in Washington where President Lincoln placed him in overall command of Union land forces. Knowing that Lee must be defeated to end the Civil War, Grant chose to make his headquarters with the Army of the Potomac in Virginia. The Grant and Lee strategic duel began in the spring of 1864 in the "Overland Campaign," also known as the "Wilderness Campaign." Starting with the Battle of the Wilderness, May 5-7, 1864, the two armies grappled continuously for many weeks through middle Virginia and the fighting was bitter and brutal. Lee was able to block every maneuver Grant made and though Lee's forces inflicted heavy losses on the Union army, Grant continued his pursuit. Lee's losses could not be easily replaced and material shortages became more acute. Despite Lee's best efforts, Grant had succeeded in continually marching Meade's Union army southward, right to the outskirts of Richmond, where Lee also had to contend with the Union Army of the James.

In mid- June, General Grant shifted his forces around Richmond to Petersburg, Virginia; an important junction for southern railroads through the Carolinas and southern Virginia. Once again, Lee's army arrived in the city to halt the Union attacks. Trenches and forts were constructed by both armies, and the battle became a siege of the city. In an attempt to break this stalemate, Lee sent part of his army northward to invade Maryland and hopefully draw off a portion of Grant's forces around the Richmond-Petersburg line. This Confederate force under General Jubal "Old Jube" Early succeeded in reaching the outskirts of Washington before they were forced to retire into Virginia. Later defeated in the Shenandoah Valley, Early's troops relinquished the valley and rejoined Lee's main force around Petersburg. “We didn't take Washington,” Early told his staff officers, “but we scared Abe Lincoln like Hell!”

Lee knew that his army could not last through a long siege but he tenaciously resisted the relentless pressure of two Union armies. In March 1865, Lee ordered one last desperate gamble to break the Union siege of the city, an attack on the center of the Union siege line. Though initially successful, the attack was repulsed by overwhelming Union firepower and Grant renewed his efforts to take Petersburg by force. The Battle of Five Forks gave the Union control of the last southern railroad into Petersburg, and the Richmond-Petersburg line was doomed. With time and odds against him, Lee ordered his army to abandon both cities. He moved his dwindling army west hoping to eventually move south to connect with Confederate forces under General Joseph Johnston in North Carolina.

Disaster followed Lee with every step of the march. Despite his best efforts, Lee knew that the end was at hand when his remaining forces were blocked near Appomattox Court House, Virginia. On April 9, 1865, dressed in his finest Confederate gray uniform, General Lee met with General Grant that afternoon to sign the terms of surrender. Lee left Appomattox and his army forever and returned to Richmond.