When
Virginia seceded from the United States, Garnett resigned his commission in April 1861 and became
Adjutant General of the Virginia troops, serving under
Robert E. Lee. In June, he was assigned as brigadier general of the Provisional Army. At the start of the Civil War,
Union forces had rapidly crossed the
Ohio River to seize a portion of northwestern
Virginia (now a part of
West Virginia), winning a key victory at the
Battle of Phillipi. On
June 15, Lee assigned Garnett to reorganize the Confederate forces in the area. He deployed his forces at strategic points along the
Staunton-Parkersburg Turnpike, hoping to defend the vital supply route from the Federal troops. A series of small battles occurred, with the Confederates being forced to withdraw under pressure from
George B. McClellan's Union forces.
After a defeat at
Battle of Rich Mountain, Garnett withdrew from his Laurel Hill entrenchments under cover of darkness, hoping to escape to northern Virginia with his 4,500 men. However, he received what later proved to be false information that his escape route to
Beverly was blocked by Union troops. He instead marched to the northeast, following ridges and valleys in a more circuituous route. Pursued for several days by as many as 20,000 Federals, Garnett paused at several stream crossings to slow his adversaries. While directing his rear guard in a delaying action at Corrick's Ford, Garnett was shot and killed during a Union volley. A friend in the Union army would recover his body after Garnett's remaining men had fled.
In recognition of Garnett's service during the
Mexican-American War, a Federal
honor guard conveyed his body under a flag of truce to his relatives, who buried Garnett in
Baltimore, Maryland. He was later re-interred next to his wife in
Green-Wood Cemetery in
Brooklyn, New York, one of two Confederate generals buried there. His headstone makes no mention of his military service, simply bearing his name and the legend "To My Wife and Child."
In
California, the General Robert S. Garnett Chapter 2570 of the
United Daughters of the Confederacy was named in his memory and honor. They funded a monument to Garnett, who had designed
California's State Seal during his brief stint serving at the Presidio in Monterey in 1849.