It had to contend with an invading Confederate force during the New Mexico Campaign of the American Civil War from mid-1861 to early 1862, then with Apache tribes during the remainder of the conflict.
Lieutenant Colonel John Baylor, commander of a battalion of the 2nd Texas Mounted Rifles, moved into the territory on July 23 and by the next evening had arrived outside of Fort Filmore, near the settlement of Mesilla.
However, the Union column quickly lost its cohesiveness during the hot daylight hours, so that when it reached San Augustine Springs Lynde reported that not "more than 100 men of the infantry battalion"[3] could offer effective resistance.
Confederate general Henry H. Sibley raised a brigade of Texas cavalry over the summer of 1861 and brought it to New Mexico in late January and early February 1862.
[6] Intending to invade Colorado to seize the gold and silver mines located there, Sibley arrived outside Fort Craig on February 15.
After a day of both sides resting and receiving reinforcements, on March 28 the Confederates advanced down the canyon and attacked the united Union force commanded by Slough.
Now having the Fort Union force in addition to his own, Canby followed the Confederates to the town of Peralta on February 17, where he fought a day- long skirmish which resulted in a few casualties but nothing else.
[10] During this time, a command of regular army units and California volunteers were organized at Fort Yuma on the Colorado River in order to defeat the Confederate invasion.
Continuing towards the Rio Grande, Carleton made contact with Canby's force on June 29; he then advanced over one hundred miles into Texas.