Department of the Missouri The Department of the Missouri was a command echelon of the United States Army in the 19th century and a sub division of the Military Division of the Missouri that functioned through the Indian Wars . History . Background . Following the successful conclusion of the Mexican - American War , the administration of the United States Army was theoretically directed , under the President of the United States , by the Secretary of War and the general in chief . In practice the Secretary of War and the heads of the army ' s staff agencies — who reported directly to him ( adjutant general , quartermaster general , commissary general , inspector general , paymaster general , surgeon general , chief engineer , colonel of topographical engineers , and colonel of ordnance ) — exercised full authority , leaving the general - in - chief a figurehead . With a lack of central direction , policy and strategy were " de facto " developed by the commanders of the numbered geographical departments and three division headquarters . After October 31 , 1853 the division echelon was eliminated and the six western departments consolidated into four ( Departments of Texas , New Mexico , the West , and the Pacific ) , whose department commanders employed their troops as they saw fit . The system returned to six departments in 1858 when the Department of Utah was created in January , and the Department of the Pacific split into the Departments of California and Oregon in September . Military activity affecting one department often originated in another department , preventing efficient use of limited manpower and coordination of efforts . Friction between the Secretaries of War and the generals in chief , and particularly between Jefferson Davis and Winfield Scott , obstructed reforms in the staff system that might have brought unity of command and civilian control of the military . The expansion of the army during the Civil War saw a proliferation in the numbers of geographic departments and their subordinate districts , often changing names and areas under their individual control , some departments eliminated or renamed , only to be recreated again in altered form . Departments of the Missouri and Kansas . The Department of Missouri resulted from the reorganization and breakup the Department of the West on November 9 , 1861 , after Abraham Lincoln fired John C . Frémont when he would not rescind his order emancipating the slaves of Missouri and imposing martial law on the state . David Hunter served briefly as the last commander Department of the West . The new department included Missouri , Arkansas , Illinois , Kentucky west of the Cumberland River and at times , Kansas . It briefly merged with the Department of Mississippi in 1862 , but was recreated September 19 , now consisting of Missouri , Arkansas , Kansas , and the Indian Territory . Colorado and Nebraska were added on October 11 , 1862 , and the department became generally known as the Department of the Missouri . From 1862 to 1865 the department was primarily concerned with fighting Confederates in Missouri and Arkansas . The Department of Kansas was created for a third time on January 1 , 1864 , removing major areas from the military jurisdiction of the Department of the Missouri . The new commander of the Department of Kansas , Maj . Gen . Samuel R . Curtis , had two districts ( Colorado and Nebraska ) wholly involved in Indian warfare , but Curtis was absorbed with fighting Confederates in the Indian Territory and bushwackers in Kansas , allowing his other districts , but particularly Colorado , complete autonomy . Governor John Evans and Colorado district commander Col . John M . Chivington took advantage of this lack of oversight to aggressively attack Cheyenne villages in April 1864 , igniting a major Indian war in July . Curtis created a new District of the Upper Arkansas , to wage the war but he was wholly incapable of locating his opponents . In his other District of Nebraska , the warfare was even more intense , but the forces there too weak to deal with it .