[1][2][3] In 1862, Gordon helped Jo Shelby raise a regiment of cavalry in Lafayette County, Missouri.

[1] Confederate Brigadier General John S. Marmaduke led a force including Shelby's brigade and Gordon's regiment on two raids into Missouri in early 1863.

[1] Gordon became full colonel of the 5th Missouri Cavalry when Shelby was promoted to brigadier general on December 15.

[1][2][3] In March and April 1864, Shelby's men harassed and skirmished with the Union Army force under the command of Major General Frederick Steele during his Camden Expedition, part of the Red River Campaign.

[1] The Confederates outnumbered the Union force at Marks' Mills by more than 2 to 1 and overwhelmed it, taking about 1,300 prisoners and about 240 wagons.

[3][11] Under Shelby, Gordon led his men on Major General Sterling Price's 1864 raid into Missouri from August 1864 to December 1864.

[11] Gordon's regiment made a successful attack during the battle but had to abandon their efforts and cut their way through encircling Union troops when the Confederate rear collapsed.

"[11] As the war was winding down and communications with the Trans-Mississippi Department were becoming slower and more difficult, Gordon did not receive a promotion to brigadier general.

In a gesture with little more than symbolic significance, General E. Kirby Smith, as commander of the Trans-Mississippi Department, assigned Gordon to command as a brigadier general on May 16, 1865, a month after the surrender of the Army of Northern Virginia and six days after the capture of Jefferson Davis by Union troops in Georgia.

[2][4][11][12] After E. Kirby Smith's surrender of the Confederate Trans-Mississippi Department, Gordon went with Jo Shelby and some of his officers and men to Mexico.