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Stephen's Sears Landscape Turned Red: The Battle of Antietam does a great job explaining how military geography influenced Confederate General Robert Lee to invade the Union in 1862. This invasion led to his first setback, the Battle of Antietam (Battle of Sharpsburg to Southerns) on September 17, 1862 and gave Union President Abraham Lincoln the strategic victory he needed to issue the Emancipation Proclamation.
In late August 1862, General Lee defeated the Northern commander of the Army of the Potomac, General John Pope, at the Battle of Second Bull Run (Second Manassas) outside the town of Manassass, Virginia. General Pope's defeat forced the Union army back to Washington, DC while the Confederates held northern Virginia. Three factors weighed heavily in Lee's mind: the fall harvest, Union congressional elections in November, and the need for another major victory to get the United Kingdom and France to recognize the Confederate States of America.
Lee had five choices on what to do
Stay put: Lee could have held his ground and kept the Union army in check with the threat of attack while digging in and therefore forcing another disaster Union assault. However, to do this would require the Southern Army of Northern Virginia to feed off the all ready strained farmlands of the region. This would prevent a successful harvest and deny Southern civilians much needed food.
March east and attack Washington, DC: Lee could have moved his forces east to capture the Union capital and give the Confederacy a political victory which would guarantee international recognition. However, Lee knew the ring of forts around Washington had the best heavy weapons of the time and that any assault would have most likely end in failure. A significant failure would invite an Union drive to capture the southern capital of Richmond, Virginia before the winter. Instead of winning the war, an attack to the east could have lost it.
March south and defend Richmond: Lee could have instead marched south to defend the capital of Richmond while resupplying and boosting the army with new volunteers. However, this would abandon hard fought ground north of Fredricksburg, Virginia and therefore cripple morale.
March west into the Shenandoah Valley. In between the Appalachian Mountains in western Virginia is the Shenandoah Valley. The valley was a key breadbasket for much of the South. Lee could have feed his troops here, captured Union strongholds in future West Virginia, and opened up a new front and then possibly link up with troops fighting to capture pro-Union Kentucky. However, Lee feared taxing the farms' harvest with his army's presence and realized he would be out of range of Richmond-based supplies. Finally, this would as well allow Union forces to recapture northern Virginia and harm morale.
March north into Union states and seek to destroy the Northern Army: This is what Lee did. Lee sought a victory which would destroy the Union's army fighting ability for the rest of the year, cost the Republican Party the congressional elections, allow Southern farmers to have a successful harvest, and gain international recognition for the Confederacy. Instead, Lee caused the bloodiest single-day battle in American history with 23,000 casualties on both sides.