Thomas was last seen by his wife at approximately 11:00 a.m. on May 14, 2005 at his residence in the vicinity of the 40 block of Old Boone Lane in Jackson, Tennessee. He has never been heard from again. His white 2001 Chevrolet Silverado truck with Tennessee license plates numbered NAD 850 was located twelve days later, burned in a field near Batchelor Loop and Tennessee 138 in Mercer, Tennessee. Thomas himself was not reported missing until June 1, however.

Two anonymous callers to investigators stated that Thomas was abducted from a local establishment. Based on the calls and on the fact that his truck was burned, authorities believed he met with foul play. In December 2005, Reggie Carnell James was charged with Thomas's murder. At his January 2007 trial, witnesses testified that James shot Thomas to death at James's residence between May 18 and May 26, weighted the corpse with concrete blocks, and dumped it in the Forked Deer River. The carpet and carpet pad at James's home were soaked with a substantial amount human blood, which supported the prosecution's theory. There was enough blood to determine that whoever's it was could not have survived without medical treatment. DNA testing was unable to match the blood to Thomas because the sample was degraded. James was convicted of first-degree murder and evidence tampering and was sentenced to life in prison without parole.

Thomas's remains have never been found. Foul play is suspected in his case due to the circumstances involved.