After the Union victory at Pea Ridge much of the Army of the Southwest was transferred to the Western Army Group commanded by Henry Halleck. Asboth's division was decreased to a brigade status in the Army of the Mississippi. Schaefer returned to regimental command during the siege of Corinth. During the Kentucky Campaign, Schaefer was on sick leave and his regiment was led by Lieutenant Colonel Bernard Laiboldt. When Schaefer returned to command he was once again the ranking officer in his brigade. He assumed command of the 2nd Brigade in Philip H. Sheridan's 3rd Division of the XIV Corps. During the battle of Stones River Schaefer's brigade was initially held in reserve of Sheridan's division. His men were soon on the front lines and eventually began to run low on ammunition. Not having an adequate supply on hand, Sheridan ordered his brigade commanders to fix bayonets and continue to resist the Confederate attacks. Sheridan's division was hard pressed throughout the first day of the battle and Schaefer became Sheridan's fourth brigade commander to fall in battle.