Colonel Nathaniel Lyon, now a fanatical abolitionist, is transferred in February 1861 to St. Louis in Missouri, a state sharply divided between a pro-Confederate governor, Claiborne F. Jackson, and a pro-Union legislature, with a valuable arsenal in St. Louis as the prize for the victor.

Lyon and his company are assigned to bolster the weak defenses of the arsenal, which contains 60,000 muskets, 90,000 pounds of powder, 1.5 million ball cartridges, 40 field pieces and the machinery for manufacture of arms.

Also located downtown is the Federal Sub-Treasury which houses over a million dollars in gold and silver.

As both facilities are severely under guarded, Lyon is ordered to fortify the compounds.

Arming twenty-five hundred volunteers loyal to the Union, he inducts them into Federal service as per his instructions from Washington.

The Missouri Volunteers elect Lyon general of their regiment by general consensus.

Colonel Nathaniel Lyon grows suspicious when Governor Jackson calls out the Missouri state militia, allegedly to train for home defense, and disguises himself as a farm woman to spy on the militia's camp.

Concluding that Jackson intends to use the militia to seize the arsenal for the Confederacy, Lyon gathers his command of about seven thousand men and starts on a six mile journey toward “Camp Jackson”, arriving from several directions and surrounding the camp.

Lyon demands and receives the camp's unconditional surrender.

When he parades his eight hundred prisoners through St. Louis, a riot breaks out in the city, which remains on the edge of chaos with violence erupting sporadically.

Lyon is officially promoted to brigadier general on May 17.

Lyon angrily declares war on Jackson’s State Guard under the command of General Sterling Price in June, despite Lincoln’s assurance to Southerners in his first inaugural address that the North would not initiate aggression.

Jackson responds by openly declaring for the Confederacy and calling for outright insurrection.

Lyon mounts a campaign to drive him from the state.

The focus early in the war is on two critical states: Missouri and Kentucky.

The loss of either will be a crippling blow to the Union cause.

Primarily because of the successes of Captain Nathaniel Lyon and his victory at Boonville in June, Missouri is held in the Union.

General Lyon has chased Governor Jackson and approximately four thousand State Militia from the State Capital at Jefferson City and from Boonville, where he remains, refitting and re-supplying his command until July 3, 1861.

Union Colonel Franz Sigel leads another force of about one thousand into southwest Missouri in search of Governor Jackson and his loyal troops.

Upon learning that Sigel has encamped at Carthage, Missouri on the night of July 4, Jackson takes command of the troops with him and formulates a plan to attack the much smaller Union force.

The next morning, Jackson closes up to Sigel, forms a battle line on a ridge ten miles north of Carthage, and induces Sigel to attack him.

Opening with artillery fire, Sigel closes to the attack.

Seeing a large Confederate force—actually unarmed recruits—moving into the woods on his left, he fears that they will turn his flank.

He withdraws and the Confederates pursue, but Sigel conducts a successful rearguard action.

By evening, Sigel is inside Carthage.

Under cover of darkness, he retreats to Sarcoxie.

The battle has little military significance, but the pro-Southern elements in Missouri, anxious for any good news, celebrate their first victory.

The Missouri legislature had taken up a bill for Missouri's secession from the Union on October 28; it passes two days later and is signed by Governor Jackson.

The Confederate Missouri State Guard, having consolidated forces in the northern and central part of the state, marches, under the command of Maj. Gen. Sterling Price, on the unionist stronghold of Lexington, Missouri, where Col. James A. Mulligan commands the entrenched Union garrison of about thirty-five hundred men.

Price's men first encounter Union skirmishers on September 13 south of town and push them back into the fortifications.

Price, having bottled the Union troops up in Lexington, decides to await his ammunition wagons, other supplies, and reinforcements before assaulting the fortifications.

By the 18th, Price is ready and orders an assault.

The Missouri State Guard moves forward in the face of heavy Union artillery fire and pushes the enemy back into their inner works.

On the 19th, the Rebels consolidate their positions, keep the Yankees under heavy artillery fire and prepare for the final attack.

Early on the morning of the 20th, Price's men advance behind mobile breastworks, made of hemp, close enough to take the Union works at the Anderson House in a final rush.

Mulligan requests surrender terms after noon, and by 2:00 PM, his men have vacated their works and stacked their arms.

Union casualties are 1,774 to the Confederates' 100.

The capture of Lexington further bolsters Southern sentiment and consolidates Confederate control in the Missouri Valley west of Arrow Rock.

Missourians side with the Union by a ratio of two or three to one, despite it's being a slave state with a highly organized and militant secessionist movement, thanks to the pro-slavery "border ruffians" who battled antislavery militias in Kansas in the 1850s.

Pro-Confederate Governor Claiborne F. Jackson and his small state guard under General Sterling Price had linked up with Confederate forces under General Ben McCulloch.

After victories at the Battle of Wilson's Creek and at Lexington, Missouri, Confederate forces had been driven out of the state by the arrival of large Union forces in February 1862 and are effectively locked out by defeat at the Battle of Pea Ridge, Arkansas, on March 6–8.