On June 17, 1861, Bee was appointed brigadier general of a brigade mobilized at Manassas Junction, although he was confirmed by the Confederate Senate posthumously. He was given command of the third brigade of the Army of the Shenandoah, under Brigadier General Joseph E. Johnston. During the subsequent battle, later known as the First Battle of Bull Run, on July 21, 1861, Bee said, "There is Jackson standing like a stone wall. Let us determine to die here, and we will conquer. Rally behind the Virginians!" in reference to Brigadier General Thomas J. Jackson and his men, giving rise to the name "Stonewall Jackson" and his Stonewall Brigade. No-one knows if this was meant to be complimentary or an insult regarding Jackson’s men not advancing. Bee was wounded in the stomach by a Union artillery shell and after considerable suffering, died the next day. As a result, it could not be determined whether his naming of Stonewall Jackson was intended as praise, a condemnation, or whether it was simply a misattributed quote. Bee is buried at St. Paul's Episcopal Church Cemetery in Pendleton, South Carolina.