The Confederate Army kept a garrison at Mr. Vernon after the battle of Wilson's Creek (August 10, 1861), but Union Colonel John Mills' troops routed them on Feb. 18th and 19th, that next spring in the "Rebel Flag Incident" where the Yankees took away several prisoners and the Rebel flag which had been flying over the courthouse. Three rows of Union trenches north of town (at Truitt Creek on Hwy. 39) were believed to have been dug to turn back an anticipated attack by Confederate General, Jo Shelby. Shelby's troops also had a skirmish north of town in October of '64, the same year disgraced Union Colonel "Doc" Jennison's Kansas raiders plundered the area prior to his arrest.

Three blocks south of the square on Main Street, The Presbyterian Church served as a Confederate army hospital after the battle of Wilson's Creek. Union troops later established a hospital in a building on the southwest corner of the square, where Trogdon's Insurance now stands. Union Col. (later, Major General), Franz Digel's troops rested here for two days after their defeat at Carthage on July 5th, 1861. Scores of other incidents occurred here and over 100,000 troops were through the area during the war. There were both Union and Confederate camps in the northeast part of town, and "town creek" at the north edge of town was a huge cavalry grazing area.