Sibley resigned from the US Army as he sided with the Confederacy. Placed in command of a brigade of volunteer cavalry in West Texas, Sibley dubbed his small force the Army of New Mexico and began planning a New Mexico Campaign to capture the cities of Albuquerque and Santa Fe and Fort Union on the Santa Fe Trail to establish a forward base of supply. He then intended to continue north to Colorado to capture the numerous gold and silver mines in the area as a means of replenishing the badly depleted Confederate treasury. From there, Sibley planned to join forces with Confederate Lieut. John R. Baylor, already in control of much of southern New Mexico and Arizona territories and headquartered in Tucson, AZ. Their ultimate strategy was to gain access to the warm-water ports of California and establish a badly needed supply line to the South, as the Union Navy had implemented a naval blockade from Virginia to Texas. Throughout the 1862 New Mexico campaign, his opponent was Colonel Edward Canby, formerly a comrade in arms in the U.S. Army. Some historians have said he was Sibley's brother in law, but this relation has been disputed.
Sibley was initially successful at the Battle of Valverde on 20–21 February and pressed on to capture Albuquerque and Santa Fe in the first weeks of March. Although the subsequent Battle of Glorieta Pass on March 28 ended in an apparent Confederate victory on the field, Sibley had to retreat because his supply train was destroyed and most of the horses and mules killed or driven off during the fight. At the same time, Union forces were approaching New Mexico from the west, the California Column. Glorieta Pass has been called the "Gettysburg of the West" by some authors; Sibley's retreat to the campaign's starting point at Fort Bliss in April ended the hopes of the Confederacy to stretch to the Pacific Ocean and use the mineral wealth of California and possibly Colorado.
After the failure of the New Mexico campaign, Sibley was given minor commands under General Richard Taylor about Bayou Teche in south Louisiana, commanding the "Arizona Brigade" at the battles of Irish Bend and Fort Bisland. The historian John D. Winters reports that he blundered on several occasions, not striking when instructed. Struggling with alcoholism, he was court martialed in Louisiana in 1863. Although not convicted of cowardice, he was censured.
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