In the autumn of 1859, while home on leave, he was ordered to assist in capturing John Brown, who had taken Harper's Ferry. At the head of a company of marines, he took Brown prisoner and, protecting him from a mob which would have lynched him, handed him over to the authorities. Two years later came the great trial of his life, when he was called upon to decide between North and South, between Virginia and the Union.

Lee was not a believer in slavery; he had never owned slaves, and when Custis died in 1859, Lee had carried out the dead man's desire that all the slaves at Arlington should be freed. Neither was he a believer in secession; but, on the other hand, he questioned the North's right to invade and coerce the seceding states, and when Virginia joined them, and made him commander-in-chief of her army, he accepted the trust. Shortly before, at the instance of his fellow-Virginian, General Scott, he had been offered command of the Union army, but declined it, stating that, though opposed to secession and deprecating war, he could take no part in an invasion of the southern states.

Curiously enough, the southern press, which was to end by idolizing him, began by abusing him. His first campaign was in western Virginia and was a woeful failure, due partly to the splendid way in which McClellan, on the Union side, managed it, and partly to blunders on the Confederate side for which Lee was in no way responsible; but the result was that that section of the state was lost to the Confederacy forever, and Lee got the blame. Even his friends feared that he had been over-rated, and he was sent away from the field of active hostilities to the far South, where he was assigned to command Florida, Georgia and South Carolina. He accepted the assignment without comment, and went to work immediately fortifying the coast, to such good purpose that his reputation was soon again firmly established. Early in 1862, he was recalled to Richmond to assist in its defense. He found his beautiful estate on the heights opposite Washington confiscated, his family exiled, his fortune gone.

General Joseph E. Johnston was in command of the forces at Richmond, and was preparing to meet McClellan, who was slowly advancing up the peninsula. But Johnston was wounded at the battle of Seven Pines, on May 31, and on the following day, Lee assumed command of the army. He got it well in hand at once, sent Stuart on a raid around McClellan's lines, and gradually forced the Union army away from Richmond, until the capital of the Confederacy was no longer in danger. Flushed with success, Lee threw his army to the northeast against Pope, routed him, crossed the Potomac into Maryland, threatened Washington, and carried the war with a vengeance into the enemy's country. A more complete reversal of conditions could not be imagined; a month before, he had been engaged in a seemingly desperate effort to save Richmond; now he had started upon an invasion of the North which promised serious results.

But things did not turn out as he expected. The inhabitants of Maryland did not rally to him, McClellan was soon after him with a great army, and on September 17, overtook him at Antietam, and fought a desperate battle; from which Lee, overwhelmed by an army half again as large as his own, was forced to withdraw defeated, though in good order, and recross the Potomac into Virginia. Three months later, he got his revenge in full measure at Fredericksburg, routing Burnside with fearful loss, and early in May of the following year scored heavily again by defeating Hooker at Chancellorsville. The last victory was a dearly-bought one, for it cost the life of that most famous of all American cavalry leaders, "Stonewall" Jackson, of whom we shall speak hereafter.

That was the culmination of Lee's career, for two months after Chancellorsville, having started on another great invasion of the North, on the fourth day of July, 1863, he was forced to retire from the fierce battle of Gettysburg with his army seriously crippled and with all hope of invading the North at an end. He was on the defensive, after that, with Grant's great army gradually closing in upon him and drawing nearer and nearer to Richmond. That he was able to prolong this struggle for nearly two years, especially considering the exhausted state of the South, was remarkable to the last degree, eloquent testimony to the high order of his leadership. Toward the last, his men were in rags and practically starving, but there was no murmuring so long as their beloved "Marse Robert" was with them.

On the ninth day of April, 1865, six days after the fall of Richmond, Lee found himself surrounded at Appomattox Courthouse by a vastly superior force under General Grant. To have fought would have meant a useless waste of human life. Lee chose the braver and harder course, and surrendered. He knew that there could be but one end to the struggle, and he was brave enough to admit defeat. On that occasion, Grant rose to the full stature of a hero. He treated his conquered foe with every courtesy; granted terms whose liberality was afterwards sharply criticised by the clique in control of Congress, but which Grant insisted should be carried out to the letter; sent the rations of his own army to the starving Confederates, and permitted them to retain their horses in order that they might get home, and have some means of earning a livelihood.

When Lee rode back to his army, it was to be surrounded by his ragged soldiers, who could not believe that the end had come, who were ready to keep on fighting, and who broke down and sobbed like children when they learned the truth. The next day, he issued an address to his army, a dignified and worthy composition, which is still treasured in many a southern home; and then, mounting his faithful horse, Traveller, which had carried him through the war, he rode slowly away to Richmond. He was greeted everywhere with the wildest enthusiasm, and found himself then, as he has ever since remained, the idol and chosen hero of the southern people, who saw in him a unique and splendid embodiment of valor and virtue, second only to the first and greatest of all Virginians, and even surpassing him in the subtle qualities of the heart.

As has been said, his fortune was gone, and it was necessary for him to earn a living. The opportunity soon came in the offer of the presidency of Washington College, at Lexington, where the remainder of his days were spent in honored quiet. Those five years of warfare, with their hardships and exposures, had brought on rheumatism of the heart, and the end came on October 12, 1870. He died dreaming of battle, and his last words were, "Tell Hill he must come up!"

Next to Lee in the hearts of the Southern soldiers was Thomas Jonathan Jackson, better known by the sobriquet of "Stonewall," which General Bee gave him during the first battle of Bull Run. Driven back by the Union onset, the Confederate left had retreated a mile or more, when it reached the plateau where Jackson and his brigade were stationed. The brigade never wavered, but stood fast and held the position.