1862 saw the birth of modern warfare and the transformation of Lincoln's war to preserve the Union into a war to emancipate the slaves. Episode Two begins with the political infighting that threatened to swamp Lincoln's administration and then follows Union General George McClellan's ill-fated campaign on the Virginia Peninsula, where his huge army meets a smaller but infinitely more resourceful Confederate force. During this episode we witness the battle of ironclad ships, partake of camp life, and watch slavery begin to crumble. We meet Ulysses S. Grant, whose exploits come to a bloody climax at the Battle of Shiloh in Tennessee. The episode ends with rumors of Europe's readiness to recognize the Confederacy.

The nightmarish Union disaster at Fredericksburg comes to two climaxes that spring: at Chancellorsville in May, where Lee wins his most brilliant victory but loses Stonewall Jackson; and at Vicksburg, where Grant's attempts to take the city by siege are stopped. During the episode we learn of fierce Northern opposition to Lincoln's Emancipation Proclamation, the miseries of regimental life and the increasing desperation of the Confederate homefront. As the episode ends, Lee decides to invade the North again to draw Grant's forces away from Vicksburg.