When the Civil War broke out and Thomas realized that neutrality was impossible, he agreed to organize the Cherokee to support the Confederacy. The 400 warriors he recruited formed two Cherokee companies; together with six companies of white men, many of whom were ethnic Scots-Irish, they comprised the famous Thomas' Legion of Cherokee Indians and Highlanders. It operated as an independent command directly under the Confederate Army's Department of East Tennessee. The Legion operated primarily in East Tennessee and Western North Carolina, except for a short period when they were deployed to the Shenandoah Valley.