By Michael Andrew Grissom, excerpt out of his book American Terrorists: Lincoln’s Armies in the South
Missouri, even though bordered on the north and east by northern states and having as its western border the new state of Kansas, which Congress admitted to the Union shortly after the secession of the Southern states, was largely, if not mostly, Southern in sentiment. Missouri had as its southern border Arkansas, and the southwestern corner of the state touched the Confederate Indian Territory, which later became the state of Oklahoma. Even so, the delegates attending the state secession convention voted overwhelmingly to remain in the Union, where they hoped solutions could be found without withdrawing from their compact with Washington. But on April 15, only three days after the affair at Ft. Sumter in South Carolina, when Abraham Lincoln ordered the state of Missouri and other states still in the Union to raise troops for the purpose of invading the Southern states, his order was met with revulsion, and Governor Claiborne Jackson notified the President that Missouri would not send one man to "carry on any such unholy crusade."
The Lincoln government moved fast. On May 10, Captain Nathaniel Lyon, who was in command of the U.S. Army garrison at St. Louis, quickly organized approximately 6,500 men, many of whom were German immigrants, and marched them towards the encampment of the Missouri militia, who were holding their regular yearly muster just outside the city limits. Acting upon rumors that Governor Jackson was preparing to arm the militia with guns and artillery from the state arsenal, Lyon and his hastily formed "army" surrounded the encampment and arrested the militiamen, marching them back through St. Louis to prison.
As Lyon marched his prisoners - almost 700 of them - back through the streets of St. Louis, angry citizens began shouting and throwing things at Lyon's armed soldiers. The Germans leveled their rifles and began shooting into the crowd. When the shooting stopped, twenty-eight people, including women and children, lay dead in the streets of St. Louis. The next day, more gunfire erupted, and ten people were killed. By the time the massacre ended, 75 more had been wounded.
On June 13, Lyon, who had been promoted to brigadier general, marched his Federal forces into Jefferson City, forcing the governor and other pro-secessionist lawmakers to flee to Boonville, about 45 miles northwest of Jefferson City. Four days later, the Missouri State Guard, commanded by Governor Jackson's nephew, John S. Marmaduke, was defeated by Union forces and forced to make a dash, along with the governor and the recently ousted lawmakers, for far southwest Missouri. At Neosho, on October 28, Governor Jackson and a remnant of the state's lawmakers met and passed an ordinance of secession; whereupon, the Confederacy admitted Missouri as its 12th state, and accepted elected representatives from the Jackson government into the Confederate Congress. But, by this time, Union forces were occupying almost all of Missouri, so Governor Jackson and his army withdrew from the state and rendezvoused with other Missourians at Washington, Arkansas, a city in the far southern part of the state, where they set up the Missouri government in exile.
The Union government back in Missouri installed Hamilton Gamble, a Republican, as the new governor without so much as allowing a vote of the people. He would remain governor through the rest of the War, and the state would be under virtual military rule until 1865. Provost marshals, with complete authority, were set up to control the citizens. Their dictums took precedence over local law. With the State Guard gone, the people of Missouri were completely defenseless. They dared not speak openly of their Southern proclivities, for Unionists all over the state were making lists of such people and arresting them, killing them, and burning their homes. As a result, there arose an array of irregular forces, rangers, guerilla fighters, and bushwhackers, who roamed the state from one end to the other. A few Confederate cavalry units managed to operate within the state for the first year, but eventually even those units were forced south. The people of Missouri would be at the mercy of the Federal occupation for four long years.