His squadron, flying in the bitter winter over the Bay of Biscay, suffered heavy casualties, and by the time Joe had completed his designated number of missions in May, he had lost his former co-pilot and a number of close friends.Joe refused his proffered leave and persuaded his crew to remain on for D-day. They flew frequently during June and July, and at the end of July they were given another opportunity to go home. He felt it unfair to ask his crew to stay on longer, and they returned to the United States. He remained. For he had heard of a new and special assignment for which volunteers had been requested which would require another month of the most dangerous type of flying.
...It may be felt, perhaps, that Joe should not have pushed his luck so far and should have accepted his leave and come home. But two facts must be borne in mind. First, at the time of his death, he had completed probably more combat missions in heavy bombers than any other pilot of his rank in the Navy and therefore was preeminently qualified, and secondly, as he told a friend early in August, he considered the odds at least fifty-fifty, and Joe never asked for any better odds than that.
The Secret mission on which he lost his life was described by a fellow officer after it was declassified:
Joe, regarded as an experienced Patrol Plane Commander, and a fellow-officer, an expert in radio control projects, was to take a "drone" Liberator bomber loaded with 21,170 pounds of high explosives into the air and to stay with it until two "mother" planes had achieved complete radio control over the "drone." They were then to bail out over England; the "drone," under the control of the "mother" planes, was to proceed on the mission which was to culminate in a crash-dive on the target, a V-2 rocket launching site in Normandy. The airplane ... was in flight with routine checking of the radio controls proceeding satisfactorily, when at 6:20 p.m. on August 12, 1944, two explosions blasted the "drone" resulting in the death of its two pilots. No final conclusions as to the cause of the explosions has ever been reached.Joe was posthumously awarded the Navy Cross ... and also the Air Medal ... In 1946 a destroyer, the USS Joseph P. Kennedy, Jr., destroyer No. 850, was launched at the Fore River shipyards as the Navy's final tribute to a gallant officer and his heroic devotion to duty...
The Destroyer USS Joseph P. Kennedy Jr. DD850 is now a museum in Battleship Cove, Fall River, Massachusetts.