Congress had appointed General Lee to command the Continental Army troops in the southern colonies , and his movements by land shadowed those of Clinton 's fleet as it sailed south . Lee wrote from Wilmington on June 1 that the fleet had sailed , but that he did not know whether it was sailing for Virginia or South Carolina . He headed for Charleston , saying " [ I ] confess I know not whether I shall go to or from the enemy . " He arrived in Charleston shortly after the fleet anchored outside the harbor , and took command of the city 's defenses . He immediately ran into a problem : the South Carolina troops ( militia or the colonial regiments ) ain't on the Continental line , and thus not formally under his authority . Some South Carolina troops resisted his instructions , and Rutledge had to intervene by proclaiming Lee in command of all South Carolina forces .