[5] Following the Battle of Boonville in June 1861, Federal Brigadier General Nathaniel Lyon ordered the 5th Regiment of the United States Reserve Corps to occupy Lexington.

[6] Stifel's scouts began securing or destroying boats that could be used to cross the river, and also confiscated about 200 kegs of gunpowder, 33 muskets, and two 6-pounder cannons from the area.

[9] Following their victory at Wilson's Creek on August 10, the main body of the pro-Confederate Missouri State Guard under Major General Sterling Price marched toward the Missouri-Kansas border with around 7,000 men to repel incursions by Lane's pro-Union Kansas Brigade.

[10] Federal reinforcements arrived in Lexington on September 4: the 13th Missouri Infantry commanded by Colonel Everett Peabody and a battalion of the United States Reserve Corps under Major Robert T. Van Horn.

[4] Mulligan now commanded 3,500 men, and quickly commenced to construct extensive fortifications around the town's Masonic College where it soon developed a fatal shortage of drinking water.

His superiors dispatched further reinforcements under Samuel D. Sturgis, with which Mulligan hoped to hold his enlarged position, but they were ambushed by pro-Confederate militia (alerted by a secessionist telegraph tapper) and compelled to retreat.

Skirmishing began the morning of September 12, when two Federal companies posted behind hemp shocks along a hill opposed Price's cavalry advance.

They battled Price's advance elements among the tombstones in Machpelah Cemetery south of town, hoping to buy time for the rest of Mulligan's men to complete their defensive preparations.

The two-and-a-half hour artillery duel badly diminished the State Guard's ammunition, and much of Price's ordnance supply train had been left at Osceola.

Price's cannon responded to Mulligan's with nine hours of bombardment, utilizing heated shot in an attempt to set fire to the Masonic College and other Federal positions.

[22] At the start of the battle over a hundred sick or wounded Union soldiers occupied this structure, with their medical care entrusted to a surgeon named Dr. Cooley, while Father Butler, Chaplain of the 23rd Illinois, provided for their spiritual needs.

[16] During the Federal assault on the Anderson house, Union troops summarily executed three State Guard soldiers at the base of the grand staircase in the main hall.

The Federal troops, who had sustained numerous casualties in retaking the residence, considered the prisoners to have been in violation of the Laws of War for having attacked a hospital in the first place.

One problem faced by the defenders was a chronic lack of water; wells within the Union lines had gone dry, and State Guard sharpshooters were able to cover a nearby spring, picking off any man who tried to approach it.

On the 20th a cannonball, probably fired from Captain Hiram Bledsoe's State Guard Battery, struck the courthouse only about one hundred yards from General Price's headquarters.

[25][26][27] On the evening of September 19, soldiers of Brigadier General Thomas A. Harris's 2nd Division (State Guard) began using hemp bales seized from nearby warehouses to construct a moveable breastwork facing the Union entrenchment.

Harris's plan was for his troops to roll the bales up the hill the following day, using them for cover as they advanced close enough to the Union garrison for a final charge.

As the fighting progressed, State Guardsmen from other divisions joined Harris's men behind them, increasing the amount of fire directed toward the Union garrison.

Although the defenders poured red-hot shot into the advancing bales, their soaking in the Missouri River the previous night had given the hemp the desired immunity to the Federal shells.

Many years later, in his book The Rise and Fall of the Confederate Government, Southern president Jefferson Davis opined that "The expedient of the bales of hemp was a brilliant conception, not unlike that which made Tarik, the Saracen warrior, immortal, and gave his name to the northern pillar of Hercules.

[29] The surrendered Union soldiers were compelled to listen to a speech by the deposed pro-Confederate Missouri governor Claiborne F. Jackson, who upbraided them for entering his state without invitation and waging war upon its citizens.

Price was reportedly so impressed by the Federal commander's demeanor and conduct during and after the battle that he offered Mulligan his own horse and buggy, and ordered him safely escorted to Union lines.