The Civil War impacted the entire Trans-Mississippi. Northern and Southern soldiers clashed as far west as Arizona, while the withdrawal of U.S. Army garrison troops to fight in the east was a factor in continued conflicts with Native Americans from Minnesota to the Pacific coast. But events in the Upper Trans-Mississippi (Missouri, Kansas, the Indian Territory, and Arkansas) were particularly significant for the war’s outcome. And nowhere were political and military events more complex than in Missouri.

In April 1861 Missouri’s pro-secessionist governor, Claiborne Fox Jackson, rejected Lincoln’s call for militia to coerce the states claiming to be the Southern Confederacy. Union hopes centered in St. Louis, where Captain Nathaniel Lyon worked with loyal citizens to defend the city’s invaluable federal arsenal. On May 10 Lyon forced an encampment of Missouri state militiamen, whom he rightly suspected of secessionist sympathies, to surrender. His action sparked a riot in which civilian women and children were killed. After the state legislature re-organized the militia into the Missouri State Guard, Lyon declared war on the state government. Promoted to General, he drove the legislature from the capital, Jefferson City, and defeated the Missouri State guard in engagements at Booneville on June 17 and Carthage on July 5. His actions, however, prompted the State Guard and its field commander, General Sterling Price, to seek help from General Benjamin McCulloch in Confederate Arkansas. McCulloch invaded Missouri to assist Price, but on August 10, 1861, Lyon made a surprise attack on their combined forces at Wilson’s Creek, near Springfield. Although Lyon was killed and his army retreated, his quick action had already secured the key railway and river networks of Missouri for the Union. As the first Union general to die in combat, Lyon became a national hero and martyr for the Northern cause.

After McCulloch’s Confederates returned to Arkansas, Price advanced to the Missouri River, capturing a Union garrison at Lexington on September 20. But he lacked a system of procuring supplies, a problem that would plague the Southern cause in Missouri throughout the war. By October he had retreated to Springfield. A rump session of the state legislature meeting nearby in Neosho passed an ordinance of secession on October 31, and a few weeks later the Congress in Richmond Virginia, admitted Missouri to the Confederacy. The Lincoln administration set up a provisional government in Jefferson City, leaving Missouri with rival governments for the duration of the war. Perhaps 60 percent of the state’s residents favored the Union cause, 40 percent the Confederacy. Well over 100,000 Missourians fought for the North or South during the course of the war, serving not only throughout the Trans-Mississippi, but as far east as North Carolina.

The Union war effort focused on opening the Mississippi River. Much of this was based out of St. Louis, and to eliminate any “back door” threat, a Union army under General Samuel Curtis drove Price out of Missouri and down into Arkansas in February 1862. Price’s men reunited with McCulloch’s, and under the overall command of General Earl Van Dorn they attacked Curtis at Pea Ridge, Arkansas, on March 7. After two days of desperate fighting Van Dorn was defeated. Some of the Confederates at Pea Ridge were Cherokee. Although Confederate agents signed treaties with the Five Nations, the Civil war split the Native American population, just as it did Americans elsewhere. Many who initially enlisted for the Confederacy deserted and later supported the Union. The battle of Newtonia, fought in western Missouri, September 30, 1862, was notable because Native American units were present on both sides. Newtonia was a Confederate victory, but throughout 1863 Union forces gradually secured control of the Indian Territory. Fighting across the region left many Native civilians destitute refugees.

From the beginning African Americans saw the conflict as an opportunity to end slavery. Their hopes rose in when on August 30, 1861, when Union General John C. Fremont declared all slaves belonging to Missouri masters supporting the rebellion free. Needing the support of loyal slaveholders in Missouri and the other Border States, Kentucky, Maryland, and Delaware, Lincoln forced Fremont to rescind his emancipation proclamation. Neither Lincoln nor Congress was willing to authorize African American enlistments in the Army. In Kansas, however, events took a different course. There the First Kansas Colored Infantry, raised in defiance of the law, took to the field. Between October 27 and 29, 1862, the unit engaged guerrillas near Island Mound, in Bates County, Missouri – the first organized African American regiment to participate in combat. Meanwhile, throughout the upper Trans-Mississippi, thousands of slaves fled their masters whenever Union troops approached. Many flooded north to St. Louis, creating a refugee problem of large proportions. Following the Emancipation Proclamation of January 1, 1863, at least 8,000 of Missouri’s African American population, both free and former slaves, enlisted in the Union army.

The closing days of 1862 were marked by a brief Confederate resurgence in the upper Trans-Mississippi. General Thomas C. Hindman led an army of Missouri and Arkansas Confederates into combat at Prairie Grove, Arkansas, on December 7. He met defeat, and in the wake of his failure Confederate authorities turned increasingly to a strategy of raids.