Thomas disappeared from his father's home in Gretna, Pennsylvania on July 1, 1991. He had told his father he was going to the local high school where he worked odd jobs, but he never returned. The following day, his girlfriend received a letter from him, which was mailed locally, saying he was struggling with some things for two years and was leaving and that she would probably never see him again. He apologized for getting her in the middle of the situation and asked her to forward the letter to his father. A few days later, another letter arrived from Portland, Maine, where he wrote that he had driven 700 miles and camped out overnight to hear the loon calls, and that he had "made a mess of things." He also wrote that he would probably be dead in two days by the time the letter was received.

Thomas's family believes he was distressed by the recent break-up of his family, as his parents divorced in 1980 and his mother, whom he was close to, had moved away to another state, his sister had moved out to attend graduate school and his high school classmates had graduated and gone their separate ways. In November 1991, his car was found abandoned near Millinocket Lake in Millinocket, Maine, with his wallet, car keys and some Canadian money inside. His backpack, sleeping bag, tent, a second set of car keys, a .38 caliber pistol and his bicycle were missing. Later that month, his sleeping bag and tent were found in a trash bin and his bicycle was discovered in a remote wooded area in November 1992. The pistol has never been recovered. Some believe he planned to hike the Appalachian Trail which is not far from Millinocket, however, none of the sightings were confirmed. The case remains unsolved.