This dissertation examines Union army military government in four Southern cities and the implications of its failures and successes for the conduct of the war and for post-war Reconstruction. It argues that President Lincoln's flexibility with respect to occupation policies resulted in a lack of leadership from Washington and left each military governor on his own. However, despite different commanders with different policies, the outcomes were virtually the same in each area. Military occupation began in each of these four cities with the same assumption on Lincoln's part, that the strength of pro-rebel sentiment was tenuous and that the presence of the Union army would encourage Unionists to step forward and reassert their control over civic functions, providing a base from which Unionism could spread and weaken Confederate nationalism and bring the war to successful conclusion. Union policy at the outset was thus conciliatory. Rules enjoined Northern troops from abusing Southern civilians in their persons or property. Events soon demonstrated that these assumptions about the strength of pro-Union sentiment were incorrect. Lincoln's conviction that real Unionist support was widespread clashed with the realities the Union army faced. Conservative Whigs, the closest approximation to real Unionists, were resistant to what they perceived as social engineering on the part of the army, and so even though the bar was set low with the Ten Percent Plan, a loyal nucleus available to ease the army's role did not emerge in any of the occupied cities. The Union army, expecting pro-Union sentiment, found scarcely any and proceeded to enact policies that created a situation in which post-war Reconstruction would become more punitive. This conclusion suggests that the experience of military occupation and the rule of the military in a democratic society is inherently destabilizing, which has implications for our ways of understanding other wars, as well as future policy.