After completing Officer Candidate School (OCS),[2]: 32  Thompson served stateside and also spent a year in Korea.

His next assignment was as a platoon commander in the 2nd Battalion of the 34th Infantry Regiment, stationed in South Korea from June 1960 to July 1961.

On March 26, 1964, Thompson was a passenger on an observation plane (an L-19/O-1 Bird Dog) flown by Captain Richard L. Whitesides when it was downed by enemy small arms fire at 16°39′12″N 106°46′21″E / 16.65333°N 106.77250°E / 16.65333; 106.77250, about 20 kilometers from Thompson's Special Forces Camp near Quảng Trị, South Vietnam.

[2]: 94  On March 27, 1964, an Army officer visited Thompson's home and told his pregnant wife Alyce that he was missing.

[7] His captors pressured him to sign statements proving that the United States' involvement in Vietnam was criminal.

He had no formal military education beyond OCS and lacked even a college degree or experience as a company commander.

In addition, Thompson's marriage had been troubled even before his captivity, and his wife Alyce, believing him dead, was living with another man at the time he was repatriated.

Alyce told author Tom Philpott that she believed prison had affected her husband's mind.

Thompson said that one of the things that helped him cope with his brutal imprisonment was thinking of the fine family that awaited his return.

[2]: 430  His superiors told author Philpott that had it not been for Thompson's status as a hero, he would have been dismissed from service because of his alcoholism.

[9] Because of his recent stroke, he had a hard time speaking, so Michael Chamowitz, his close friend and lawyer, read his retirement speech.

I found that the dream of continued service gave me a goal that helped me survive my years as a POW.

January 29, 1982[10]In 1981, Thompson moved to Key West, where he remained active in the community, according to the Monroe County Office of Veterans Affairs.

[11] On July 8, 2002, the staff of Joint Interagency Task Force (JIATF) East and some of his close friends threw Thompson a birthday party.

Eight days later, on July 16, 2002, Thompson was found dead in his Key West By the Sea condominium, at the age of 69.

In an update to Glory Denied, Tom Philpott reported that Alyce Thompson died of cancer in 2009.

He also mentioned that Thompson's daughter Ruth had suffered three disabling heart attacks and had lost a son to suicide.

Philpott reported that Ruth had told him the strength of character that she inherited from both her parents had helped her though the difficult times.

[13] In recognition of his escape from a Viet Cong POW camp for two days in October 1971, Thompson received the Silver Star.