I was corresponding with Missouri author, historian, and (of course) lawyer James McGhee the other day and we were both lamenting the lack of a book length study of the period surrounding the Battle of Lexington. Missouri State Guard General Sterling Price's successful advance to the pro-Southern "Little Dixie" region astride the Missouri River after the victory at Wilson's Creek is a neglected piece of Civil War military history. Price's capture of the large brigade-sized Federal force under Colonel James Mulligan at Lexington was an impressive victory for his large but poorly trained, supplied, and equipped army. The success resulted in recruits flocking to Price's standard and perhaps represented the high water mark of Southern hopes for the state. Although several short articles have been written, the best single source remains Michael Gillespie's short booklet The Civil War Battle of Lexington, Missouri. I purchased a copy from Camp Pope a few years ago but it looks like they don't sell it there anymore. The bookstore at the Battle of Lexington State Historic Site is probably the best bet for finding a copy.
Three independent Confederate forces were in position to cooperate with Missouri State forces but proved unable or unwilling to help. Ben McCulloch, who hated Price, returned his division-sized force to Arkansas after Wilson's Creek. William Hardee's brigade-sized command in northeast Arkansas and Gideon Pillow's 6,000 man Army of Liberation at New Madrid, MO similarly declined to assist MSG General M. Jeff Thompson in the bootheel region of SE Missouri. This lack of pressure on multiple fronts allowed John C. Fremont the opportunity to concentrate against Sterling Price's guardsmen at Lexington. The large 38,000 man Union force easily herded Price back into the southwest corner of Missouri, permanently solidifying U.S. control over the state.
Jim and I both agree that mid-summer 1861 was the South's last real opportunity to accomplish something important in Missouri. However, with no overall directing hand, the combined Confederate-Missouri State Guard victory at Wilson's Creek went largely unexploited. Although I doubt that any permanent Confederate stronghold in Missouri was possible, active Confederate armies operating in Missouri in the latter part of 1861 could have had a serious effect on Union plans for the Western theater in the first months of 1862, perhaps allowing A.S. Johnston's Confederates more time to prepare river defenses in Tennessee. In January of 1862, with only a weak enemy presence in Missouri, Union Department of the Missouri commander Henry Halleck had over 70000 men stationed in the state, leaving only around 20000 men with Grant east of the Mississippi. With a graver threat to Missouri, would Halleck have even authorized the Henry-Donelson thrust?
Once this summer 1861 window of opportunity passed, all possibility of sustaining a strong Confederate presence in Missouri evaporated. The Missouri River ran east-west across the middle part of the state and the Federal army controlled the railroads, all of which exited Missouri only into Northern states. The fact that Missouri was hemmed in geographically by free states on three sides didn't help either. Unfortunately for the Confederacy, Missouri's natural and man-made supply and communication network could only help Union armies and the many fortified strongpoints constructed by the Federals could not be taken by the South's mobile but equipment starved and logistically poor upper Trans-Mississippi theater forces.