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In Feb., 1861 (after the secession of the lower South), General Scott, with whom Lee was a great favorite, recalled him from Texas. Lee had no sympathy with either secession or slavery and, loving the Union and the army, deprecated the thought of sectional conflict. But in his tradition, loyalty to Virginia came first, and upon Virginia's secession he resigned (Apr. 20, 1861) from the army. His resolve not to fight against the South had already led him to decline (Apr. 18) the field command of the U.S. forces.
On Apr. 23 he assumed command of the military and naval forces of Virginia, which he organized thoroughly before they were absorbed by the Confederacy. Lee then became military adviser to Confederate President Jefferson Davis and was made a Confederate general. After the failure of his efforts to coordinate the activity of Confederate forces in the western part of Virginia (July–Oct., 1861), Lee organized the S Atlantic coast defenses.
In Mar., 1862, Davis recalled him to Richmond. Lee's plan to prevent reinforcements from reaching Gen. George B. McClellan, whose army was threatening Richmond, was brilliantly executed by T. J. (Stonewall) Jackson in the Shenandoah Valley. When Joseph E. Johnston was wounded at Fair Oaks in the Peninsular campaign, Lee assumed command of the Army of Northern Virginia (June 1, 1862). His leadership of that army through the next three years has placed him among the world's great commanders.
Lee immediately took the offensive, and after ending McClellan's threat to Richmond in the Seven Days battles (June 26–July 2), he thoroughly defeated John Pope at the second battle of Bull Run (Aug. 29–30). McClellan, however, checked him in his first Northern invasion, the Antietam campaign (Sept.). Advances by Ambrose E. Burnside and Joseph Hooker were brutally repulsed in the battles of Fredericksburg (Dec. 13; see Fredericksburg, battle of) and Chancellorsville (May 2–4, 1863), though in the latter victory Lee lost his ablest lieutenant, Stonewall Jackson.
Lee's second invasion of the North resulted in the Confederate defeat in the Gettysburg campaign (June–July). He sorely missed the services of Jackson, and some historians attribute his defeat at Gettysburg to the failures of his subordinates, particularly James Longstreet. Other authorities argue that Lee underestimated his opposition and failed to impose his will upon his subordinates. Lee assumed full blame for the defeat, but Davis refused to entertain his offer of resignation. After Gettysburg, Lee did not engage in any major campaign until May, 1864, when Ulysses S. Grant moved against him. He repulsed Grant's direct assaults in the Wilderness campaign (May–June), but was not strong enough to turn him back, and in July, 1864, Grant began the long siege of Petersburg.
Lee's appointment as general in chief of all Confederate armies came (Feb., 1865) when the Confederacy had virtually collapsed. On Apr. 2, the Army of the Potomac broke through the Petersburg defenses, and Lee's forces retreated. One week later Lee surrendered to Grant at Appomattox Courthouse (see under Appomattox).
After the war Lee became president of Washington College (now Washington and Lee Univ.). Although President Andrew Johnson never granted him the official amnesty for which he applied, Lee nevertheless urged the people of the South to work for the restoration of peace and harmony in a united country.
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