On March 26, 1964, the Air Force observation plane flown by Capt. Richard L. Whitesides and co-piloted by Thompson was hit and disabled by small arms fire outside their Special Forces Camp near Quang Tri, South Vietnam.  Suffering burns, a bullet wound across the cheek and with his back broken, Thompson survived the initial crash, but was captured by the Viet Cong. Whitesides, although said by the Viet Cong to have been killed, has never been found. 

For next nine years as a prisoner of war in Vietnam, Thompson was subjected to constant mental and physical torture at the hands of his Viet Cong captors. Largely kept isolated from others, he was first held in crudely constructed jungle cages and later in cold prison cells, ending up in the infamous Hanoi Hilton. Leaving for Vietnam the day after Christmas in 1963, Thompson had orders for a six-month assignment out of Fort Bragg, N.C. When Thompson told his mother he was being shipped out to Vietnam for a temporary tour of duty, she asked, "Where the hell is that?" He replied, "I don't know."  Leaving his wife of nine years, Alyce, and three daughters, he had been in Vietnam less than three months when he was captured.

The day after Thompson was reported as being shot down, an Army officer paid a visit to the Thompson home to notify Alyce Thompson. Rocked by the news her husband was listed as missing in action, the pregnant Alyce Thompson went into labor, giving birth to the couple's only son. In the first months of captivity, the injured Thompson rapidly lost weight and suffered his first attack of malaria. His mental toughness made the Special Forces soldier realize he needed to take care of himself in order to survive. He disciplined himself to ignore the agonizing pain he was experiencing, and within three months recovered to the point where he could sit and walk. 

However, his recovery was brief, as Viet Cong interrogators relentlessly subjected Thompson to more torture. It was while at the Hanoi Hilton that Thompson made a reported five attempts to escape. On one occasion, Thompson and a Naval civilian employee tried to flee to freedom. Recaptured two days later, Thompson's captors escalated the torture sessions.  Nearly killed by his ordeal, Thompson reluctantly signed a propaganda  tatement saying he was being treated well. He was released in March 1973, as a part of Operation Homecoming.

Returning to U.S. soil, Thompson faced many of the countless hurdles confronting others held in captivity, including to two failed marriages, a battle with alcoholism, a heart attack and a debilitating stroke.