This unit has such a problematic history that one can never be absolutely sure how it started, what all it accomplished, who all served, and who all led it, including when and where. Col. William Holland Thomas organized "Thomas's Cherokee Battalion" in Jackson County, NC on July 19, 1862, and by October 1, 1862, he had created a full regiment - soon to be called "Love's Regiment-Thomas's Legion" or the "Infantry Regiment-Thomas's Legion," and another Battalion - soon to be called "Walker's Battalion-Thomas's Legion." These units served mostly in Eastern Tennessee and somtimes in Western North Carolina until May of 1864 when they were ordered to the Shenandoah Valley of Virginia..

On September 2, 1863, Col. William H. Thomas took two (2) companies from "Love's Regiment-Thomas's Legion" back into North Carolina to help protect the people of Cherokee, Clay, Macon, Jackson, and Haywood counties. Col. Thomas planned to use the original Indian Companies from the "Infantry Regiment" as a nucleus around which to raise more Cherokee Companies. It is clear that the new companies included many whites, however, the majority of the new recruits were indeed Cherokees or part Cherokee. Also part of his plan was to fill new companies with men who had either deserted earlier or were absentees from other regiments and/or battalions. There is also evidence that part or all of Company K of the 5th TN Cavalry joined Col. Thomas by the Spring of 1864 and was pulled into one of the new companies of what was now being called the "Indian Battalion-Thomas's Legion."

Although not formally organized yet, the "Indian Battalion-Thomas's Legion" served almost exclusively in the five (5) counties named above in Western North Carolina. However, Col. Thomas could not pass up favorable opportunities in the adjacent Eastern Tennessee counties when it suited him. On December 8, 1863, he and his Indian Battalion-Thomas's Legion raided Sevierville, TN to rescue some of his men from jail, and two (2) days later, on December 10, 1863, the Indian Battalion was assaulted by two Union cavalry units at Gatlinburg, TN.

On February 2, 1864, the 14th IL Cavalry surprised Col. Thomas's camp on Deep Creek, NC. Accounts vary widely. Some say the Indians gave stiff resistance until their ammunition ran out. One newspaper account turned things around and claimed Col. Thomas was the one who surprised the Federals. Another account asserts that Col. Thomas's men were soundly beaten.

In the meantime, several factions attempted to coerce Col. Thomas to bring all his men back to the "Infantry Regiment" and rejoin that regiment and Walker's Battalion-Thomas's Legion in Eastern Tennessee; some requesting, others demanding. Lt. Col. James R. Love was sympathetic with Col. Thomas, but he too wrote many letters to Col. Thomas asking him to return to Eastern Tennessee. With the murder of Lt. Col. William C. Walker of "Walker's Battalion-Thomas's Legion" on January 3, 1864, the entire "Legion" was in great turmoil, and many officers wrote a petition to Governor Zebulon B. Vance on February 25, 1864 for assistance in re-uniting Thomas's Legion and removing it from Brig. Gen. Alfred E. Jackson's (TN) command.

In May of 1864, "Love's Regiment-Thomas's Legion" and "Walker's Battalion-Thomas's Legion" were sent to the Shenandoah Valley in Virginia to support Lt. Gen. Jubal A. Early (VA) in his Valley Campaigns of 1864. Col. William H. Thomas remained in Western North Carolina with his informal "Indian Battalion-Thomas's Legion" all this time, with very little documentation available as to their service. Love's Regiment-Thomas's Legion and Walker's Battalion-Thomas's Legion returned to Western North Carolina in November of 1864 (some say December). Many of the men with Col. Thomas who were absentees from other Legion units possibly returned to their old companies at this time.

On October of 1864, part of the Indian Battalion-Thomas's Legion was with Col. John B. Palmer (Western District of North Carolina Assistant Commandant, now under Brig. Gen. James G. Martin) when he moved into Cocke County, TN to prevent the Federals from coming into North Carolina. Col. Palmer moved from Asheville to Warm Springs on October 17, then crossed Paint Mountain on October 19, 1864 with 800 men, consisting of the 62nd NC Regiment, the 64th NC Regiment, a three-gun battery, and a contingent of the Indian Battalion-Thomas's Legion under the command of Capt. Matthew H. Love of Company A. This group consisted of the white companies of the Indian Battalion only: Capt. Matthew H. Love's Company A, Capt. John D. Berry's Company D, Capt. Albert L. Hicks's Company F, and Capt. DeWitt C. Ghormley/Capt. Eppa Everett's consolidated Company G. Col. Palmer wrote "I have brought no Indians with me, General Martin having prohibited me doing so."

Col. Palmer was ordered to join Brig. Gen. John C. Vaughn (TN) at Morristown, TN on October 27th, where skirmishing was in progress. Col. Palmer's initial efforts to halt the retreating allies as they passed him by. Brig. Gen. Vaughn finally managed to rally a samll part of his force in the rear, and Col. Pamer's guns halted the federals, who withdrew.

Col. Thomas appears to have gathered the Indian Companies together separately by February of 1865, and he received authorization to formally organize them into a new Battalion on April 9, 1865. Since this was so close to the "final chapter" of the American Civil War, complete rosters for the Indian Battalion-Thomas's Legion are not available. There are hints in some records that two (2) companies of the so-called Indian Battalion-Thomas's Legion actually joined Love's Regiment-Thomas's Legion, and one (1) company joined "Walker's Battalion-Thomas's Legion" as early as March of 1865, before the Indian Battalion-Thomas's Legion was formally authorized. Did they remain, or did Col. William H. Thomas yank them back to his command? The exact size of Col. Thomas's Western North Carolina command and how it evolved is now impossible to fully straighten out.

Early historians of Thomas's Legion did nothing to untangle this issue, perhaps because they never fully understood how complicated it was. As provided in the histories of "Love's Regiment-Thomas's Legion," and "Walker's Battalion-Thomas's Legion," Editor Walter Clark incorrectly called the former as the 69th NC Regiment, and the latter as the 80th NC Regiment. In these narratives, it is clear that the authors simply ignored the "Indian Battalion-Thomas's Legion," and it seems that some companies were conflated with other companies in Walker's Battalion-Thomas's Legion (which never became a full regiment as some claimed).

To make matters worse, when detailed researchers finally got their hands on better records, it became clearer that many men who were considered AWOL from "Love's Regiment-Thomas's Legion" and "Walker's Battalion-Thomas's Legion" were actually serving in the "Indian Battalion-Thomas's Legion," so they were technically not truly AWOL. Incomplete records have been located for rosters from April of 1864 until early 1865, and includes seven (7) of the eight (8) companies identified above. There are also scant records for one more company which Col. Thomas attempted to organize in August-September of 1864, but which may have never come together completely.

On May 9, 1865, Brig. Gen. James G. Martin (NC) - Commandant of the District of Western North Carolina - met with Federal Col. William C. Bartlett in Waynesville, NC to discuss surrender. With him were Col. James R. Love and Col. William H. Thomas, the latter accompanied by twenty (20) Cherokee "stripped to the waist and painted and feathered in good old style." According to some sources, Col. Thomas threatened Col. Bartlett and his men with scalping if they did not retreat, but cooler heads prevailed. After negotiations, Thomas's Legion and the rest of Brig. Gen. James G. Martin's command surrendered Waynesville on May 10, 1865 (some sources say May 7th), a full month after General Robert E. Lee (VA) surrendered at Appomattox Court House, VA.

The members of Col. Thomas's Life Guard, who were not in Confederate service, were allowed to retain their arms, as wer some other Cherokees whom Col. Thomas claimed were not involved in the war; arguing that it was necessary for them to keep their weapons to protect their families from ther marauder bands still roaming Western North Carolina. Meanwhile, many of the Indian Battalion-Thomas's Legion simply slipped away with their weapons, but the majority turned in their weapons and surrendered.