After his general's death, Hotchkiss continued to be assigned to the staff of the corps commanders who succeeded Jackson (Generals Richard S. Ewell and Jubal A. Early), but he was frequently called upon to work directly for General Robert E. Lee at the headquarters of the Army of Northern Virginia. Balancing these dual responsibilities, he served through the Gettysburg Campaign, the Mine Run Campaign, and the Overland Campaign. In June 1864 he accompanied General Early on his raid through the Shenandoah Valley toward Washington, D.C., and one of his maps contributed to Early's successful surprise attack against General Philip Sheridan at the Battle of Cedar Creek (although the map was not able to prevent Early's decisive defeat by the end of the battle). He then returned to the Siege of Petersburg with the remnants of Early's defeated army for the remainder of the war.