In 1965, Thorne transferred to Military Assistance Command, Vietnam – Studies and Observations Group (MACV–SOG). This was a classified U.S. special operations unit. The unit focused on unconventional warfare in Vietnam. On 18 October 1965, Thorne was supervising a secret mission on a helicopter. The helicopter crashed in a mountainous area of Vietnam, 25 miles (40 km) from Da Nang. A rescue team went to the crash site. They could not find it because of the mountains and trees.