He completed 25 missions as pilot of a land based PB4Y patrol bomber by 1944 and was eligible to return home to the United States.
The bomb filled planes couldn't safely take off by remote control; pilots had to take off and fly them up to 2000 feet where the remote control would take over and the pilots would parachute out of the plane. The planes would then be crashed into the target.
On August 12, 1944, five planes took off from RAF Fersfield near Norwich in Norfok, England. The BQ-8 (a converted remote control equipped B-24 Liberator) was piloted by Joe Kennedy; his co pilot was Lt. John Willy. Two of the other planes were Lockheed Venturas, the navigation plane was a B-17, and an F-8 Mosquito was the photography plane.
Their target was the Fortress of Mimoyecques, an underground German military complex in the Pas-de-Calais region of northern France. The allies knew something was going on there, but they didn't know that the site was supposed to house 25 giant V3 cannons which the Germans hoped to use to bombard London (only a hundred miles away).
Kennedy's plane was loaded with 21,000 pounds of Torpex and the plan was for Kennedy and his co pilot to get the plane into the air, put the plane on remote control for a test turn, remove the explosive firing pin, and then parachute to safety before the plane was guided to its target.
Everything went according to plan up to and including the firing pin removal. Over the radio, Kennedy told the other planes, that the pin had been removed. Two minutes later, the plane exploded.
A camera man in the photography plane who was injured by some of the fragments from the explosion says,
the Baby just exploded in mid-air as we neared it and I was knocked halfway back to the cockpit. A few pieces of the Baby came through the plexiglass nose and I got hit in the head and caught a lot of fragments in my right arm. I crawled back to the cockpit and lowered the wheels so that Bob could make a quick emergency landing,
Kennedy and his co pilot were killed instantly. Later, an electronics officer said he had warned Kennedy the day before the flight about a possible defect in the wiring harness.
Kennedy's father and the rest of the family were devastated by Joe's death. The presidential plans that Joesph Kennedy senior had for Joe Junior were passed on to the next oldest son, John F. Kennedy.