The area has a rich geologic history (PDF map). Millions of years of water advances, retreats, and land uplift created mountains. The most important factor though to Harpers Ferry was the cutting of the rock by water. Both the present-day Potomac and Shenandoah Rivers managed to carve the landscape and meet up where the town is now located. The rivers were able to cut through most of the rock while harder rocks fell into the river.
The meeting of the two rivers created an prime place for settlement in the years right before the American Revolution. A ferry allowed land transport because while the rivers were still wide enough for boat travel rapids blocked access. The town was considered the last place of civilization before the great American wilderness.
George Washington scouted the area for canal improvements after the war and fell in love with Harpers Ferry. When Washington became president he saw a use for Harpers Ferry; the town was sixty miles away from the future capital and would provide a good fall back point in case of invasion. So Washington established a federal armory at Harpers Ferry. The armory contained over 10,000 guns and plenty of supplies to wage war.
The munitions at Harpers Ferry attracted interest. John Brown, the anti-slavery zealot wanted in Kansas for murder, decided to bring the fight for freedom to the east. Working with members of his Kansas militia Brown trained for a raid into the town to seize the armory in 1859. It failed. After the raid it was revealed Brown had financial backing from Northerners and plotted to start slave rebellions all throughout the South. What was most frightening was that the attacked happened in the east ("close to home" and not out in the wild country of Kansas). These facts scared almost every military-age Southerner into militia training. The training helped Southerners win battles and prolong the Civil War by years. Hundreds of thousands would die because of the skills Southerners learned because of the raid.
In a series of connections the millions of years of geomorphology helped start and prolong the Civil War. In geography, like Harpers Ferry, everything is interconnected.