Dewey arrived on September 4, 1945 in Saigon to head a seven-man OSS team 'to represent American interests' and collect intelligence. Working with the Viet Minh, he arranged the repatriation of 4,549 Allied POWs, including 240 Americans, from two Japanese camps near Saigon, code named Project Embankment. Because the British occupation forces who had arrived to accept the Japanese surrender were short of troops, they armed French POWs on September 22 to protect the city from a potential Viet Minh attack. In taking control of the city, the French soldiers were quick to beat or shoot Vietnamese who resisted the reestablishment of French authority.

Dewey complained about the abuse to the British commander General Douglas Gracey, who took exception to Dewey's objections and declared the American persona non grata. Because the airplane scheduled to fly Dewey out did not arrive on time at Tan Son Nhut International Airport, he returned for lunch at the villa that OSS had requisitioned in Saigon. As he neared the villa, he was shot in the head in an ambush by Viet Minh troops.

The Viet Minh afterward claimed that their troops mistook him for a Frenchman after he had spoken to them in French. According to Vietnamese historian Tran Van Giau, Dewey's body was dumped in a nearby river and was never recovered. Reportedly, Ho Chi Minh sent a letter of condolence about Dewey??? death to President Truman while also ordering a search for the colonel's body.