Thomas is referred to as "Chief by the Cherokees" and considered savior of over 1000 Cherokees during the bloody Trail of Tears, which the Cherokees refer to as Nunahi-Duna-Dlo-Hilu-I or Trail Where They Cried. Principal Chief of the Cherokee Nation, John Ross, had lost his wife Quatie during the infamous Indian Removal. Thomas was in Washington during the Treaty of New Echota negotiations and he successfully lobbied for the right of a number of Indians to remain in North Carolina, and these Indians are the present-day Eastern Band. They were also called Oconaluftee, Lufty and Qualla Indians. In the late winter of 1839, while Thomas was in Washington, Yonaguska died. Thomas learned about it in April. Before his death, the old chief had summoned the men in his band to form a circle around his pallet in the Soco Council House. They accepted his recommendation that "Little Will" be allowed to succeed him. Yonaguska then advised them to abstain from drinking liquor and never to move west...William Holland Thomas became Chief of the Oconaluftee Indians and he was the only white man to hold that office. Also see Cherokee War Rituals, Culture, Festivals, Government, and Beliefs.

The Western North Carolinians had fought the Cherokees for decades, and if the Cherokees fight in the American Civil War will they join the North? Or will they remain neutral? On the other hand, the Cherokees had entered into six separate treaties with the U.S. government between 1777 and 1835. In each case, federal authorities had sought to extend the frontiers of white settlement by extinguishing Indian title to land. The United States had broken several promises, including President Andrew Jackson's unconscionable betrayal of Chief Junaluska and his Cherokees. The great warrior and chief had saved General Jackson's life at the Battle of Horseshoe Bend and subsequently, when "Old Hickory" was elected the 7th President, he forced the Cherokees from their homeland. But by the 1860s, the highlanders and Cherokees were neighbors and, moreover, friends. Cherokee intermarriage with neighboring whites was also more common. Furthermore, prior to his death, Yonaguska commanded his people to obey Chief Thomas. In 1883, Ziegler recorded that "before Yonaguska died he assembled his people and publicly willed the chieftainship to his clerk, friend and adopted son, W. H. Thomas, who he commended as worthy of respect and whom he adjured them to obey as they had obeyed him. He was going to the home provided for him by the [G]reat [S]pirit; he would always keep watch over his people and would be grieved to see any of them disobey the new chief he had chosen to rule over them." General Winfield Scott and the United States Army (enforcing Andrew Jackson's Indian Removal Policy) had eradicated the Cherokees during the removal termed  Trail of Tears. The Indians vividly remembered Jackson's betrayal and the 4000 Cherokees that perished (also see Cherokee Declaration and the American Civil War and American Indians in the Civil War). And in the beginning of the American Civil War, General Scott was appointed General-in-Chief of the Union Army; he was also a veteran of the War of 1812, hero during the Mexican-American War, former presidential candidate, and during the Civil War was credited for his superb Anaconda Plan. Other notable soldiers of the Mexican-American War: Robert E. Lee, Braxton Bragg, U. S. Grant, "Stonewall" Jackson, Zachary Taylor, and Jefferson Davis.

According to Neely, North Carolina's Eastern Band of Cherokees, p. 162, "Some Cherokees desired neutrality while as many as 30 joined the Union Army." Oral history states that many of the disloyal Cherokees were later murdered by their relatives because they betrayed their Chief, Thomas. The Indians that joined the Union Army not only fought against their brothers, but after the War are credited for returning to Western North Carolina with the dreaded smallpox. Captured Confederate Cherokees, however, were held in Federal prisoner of war camps and after the War, the paroled Cherokees, immediately returned to Western North Carolina and, most likely, also with smallpox. Smallpox is considered biological warfare and is currently deemed a Weapon of Mass Destruction or WMD. Not combat, but mumps, measles and, after the War, smallpox were responsible for killing hundreds of Cherokees (Thomas's letter concerning smallpox). On September 15, 1861, two Cherokee companies (200 warriors) loyally answered the call to arms. These 200 Indians were originally known as the Junaluska Zouaves (in honor of Chief Junaluska), and Thomas also referred to them as the North Carolina Cherokee Battalion (O.R., Series 1, 51, II, p. 304 and O.R., 1, 49, Part 2, p. 754). By the end of the war, muster records reflect almost every able-bodied Cherokee, about 400 soldiers, from Western North Carolina entered into Confederate military service, and their loyalty was to Chief Thomas and then to the Confederacy. And in O.R., 1, 53, p. 314, Thomas stated that the Cherokees didn't own any slaves, so slavery wasn't a motive. 

 President Jefferson Davis's Cousin and Friend

Will Thomas's American Civil War Strategy

William Thomas strongly believed in defensive guerrilla warfare and, since the Union army typically outnumbered the Confederate army by more than two-to-one, Thomas wisely opposed the traditional Napoleonic Linear Tactics. Will was not a Fire-Eater, he initially opposed secession, and during the war a $5,000 bounty was offered to anyone that would assassinate the Confederate Chief.

"Many of them [Thomas' Legion] joined with the promise that they were not to be taken out of the State except in the North Carolina mountain of defense." Captain Robert A. Akin, Company H, Walker's Battalion, Thomas' Legion

The mountaineers, like their Overmountain forefathers during the American Revolution, vehemently believed in a defensive war. Their mountain ancestors proved their defensive strategy by surprising and destroying the British Army at two key southern battles: the Battle of Kings Mountain and the Battle of Cowpens. Who knew the Western North Carolina geography and topography better than the indigenous Cherokees and Mountaineers? Thomas petitioned Richmond to authorize the recruitment of "additional Indians and such whites as I may select." His primary goal was to recruit a full battalion and ultimately a mounted regiment to operate as an independent guerrilla force for the "local defense of the Cumberland Gap in pro-Unionist East Tennessee and Western North Carolina." According to William Holland Thomas's writings, Jefferson Davis agreed to arm, supply, and support the unit. In future correspondence with Jeff Davis, Thomas stated, "I have increased the Battalion of Indians and Mountaineers to a regiment and am progressing with a Legion. Not for one year but for three years or during the war." (North Carolina Division of Archives and History, April 17, 1862; and Vernon H. Crow, Storm in the Mountains: Thomas' Confederate Legion of Cherokee Indians and Mountaineers, 12-36.) Consequently,  Thomas wrote to President Davis and "submitted a plan for the defenses of East Tennessee." November 8, 1862, Strawberry Pains, TN. (O.R., Ser. I, Vol. 20, pt. II, p. 395) 

General Ulysses S. Grant, traveling through the Cumberland Gap in 1864 noted: "With two brigades of the Army of the Cumberland I could hold that pass against the army which Napoleon led to Moscow."