Waggoner last spoke to his family on October 9, 1971 from Pasadena, Texas. He has never been heard from again. He apparently took with him only his wallet and a .9 millimeter pistol. His car, with the key in the ignition, was found parked in front of his apartment on Lafferty Street in Pasadena, and some clothes, Waggoner's suitcase, and a small amount of money were left inside his home.

A hunter located Waggoner's red Honda 350 motorcycle in the woods off U. S. Highway 59 in Cold Springs, Texas, seventy miles north of Houston, Texas, approximately two weeks after his initial disappearance. His helmet was sitting on top of it. There has been no trace of Waggoner since that time.

Waggoner's family believes he may have been accosted by James "Humpy" Parker, then the sheriff of San Jacinto County, Texas. Parker and several of his deputies later went to prison for detaining and torturing young men they met on U. S. Highway 59. In particular, they liked to target men who rode motorcycles. They have not been linked to Waggoner's case, however, and Parker is now deceased.

Waggoner served four years in the United States Marines. He was unemployed at the time of his disappearance; he quit his last job several weeks before he went missing because it bored him. He was close to his parents, who lived nearby, and his sister, and his loved ones do not believe he would have left without warning. They also stated he was not depressed or suicidal in 1971. Waggoner's parents are now deceased, but his sister is still searching for him. Authorities believe he may have been taken against his will.