On August 9, 1945 the second atomic bombing mission was launched. The target was the city of Kokura, with Nagasaki, a seaport and a vital part of the military industrial power of Japan, as the secondary. Fat Boy was being flown in Bockscar, commanded by Major Charles W. Sweeney. Kokura was obscured by clouds and by smoke from a nearby US fire bombing raid. After three abortive bombing runs over Kokura, and with fuel running low from a failed fuel pump, Bockscar headed for Nagasaki.
Nagasaki too, was largely obscured by clouds. At 11:01 AM, a break in the cloud cover allowed the dropping of the bomb. Fat Man exploded 47 seconds later over a tennis court, halfway between the Mitsubishi Steel and Arms Work and the Nagasaki arsenal. The blast was confined to the Urakami Valley and the rest of Nagasaki was protected from the initial blast by the hills around the valley. Immediate deaths on the ground are estimated from 22,000-75,000.
Bockscar due to the fuel leak, had to make an emergency landing on Okinawa with about five minutes of fuel to spare.
Contrary to mythology popular among more paranoid Catholic circles, Nagasaki was not chosen in an evil Masonic plot by Truman to wipe out Japanese Catholicism. Urakami Cathedral was not the aiming point for the bomb. The Cathedral was destroyed because the bomb missed its aiming point by half a mile and exploded 500 feet from the Cathedral.
The Japanese Supreme War Council were conference at the time of the bombing, deadlocked between peace and war factions. Unable to break the deadlock, even after having received the news on Nagasaki, it was decided that the deadlock would be brought to the attention of the Emperor for him to resolve.