Nagasaki was the most Christian city in Japan, probably the most Catholic city in Asia outside the Philippines. Urakami Cathedral was less than 500m from Ground Zero.
Nagasaki was not the primary target of Special Mission No. 16. It had not even been on the original list of four possible targets, but replaced Kyoto reportedly after a world-travelling friend happened to tell Henry Stimson, the Secretary of War, how beautiful Kyoto was.
The mission was one near-disaster after another. Shortly before the flight Maj. Charles Sweeney was informed that due to a malfunctioning pump the 600 gallons of reserve fuel would not be available. Sweeney chose to go ahead with the mission. Shortly after takeoff a warning light on the black box which monitored the bomb's electrical circuitry went off. Two switch positions had been reversed. Had it been one of the timing fuses the bomb would have gone off in 53 seconds. It took more than that to find the problem. Then the camera plane missed the rendezvous point, causing a 45-minute delay. Sweeney probably wouldn't have waited that long had he known the camera operator had missed the flight, but they were maintaining strict radio silence.
The primary target was the arsenal at Kokura. The clear skies reported by the observation planes was now filling with broken clouds. Under orders to drop the bomb visually only--not by radar--the bombardier was able to make out landscape features, but the target was obscured by smoke from a nearby factory which had been bombed two days earlier. Three bomb runs from two different directions were aborted, under increasingly heavy flak. Kokura was one of the best defended cities in the Empire.
The delay had also allowed a cold front to move in on Nagasaki. There was fuel for one bomb run only if they were to make it to Okinawa. The decision was made to drop the bomb by radar, contrary to orders, but the bombardier found a hole in the clouds near the secondary target, the Mitsubishi Steel Works in the Urakami Valley. The bomb exploded at 1600 feet at 1102 hours, August 9, 1945.
There's no way of knowing how many people were killed by the bomb in either Hiroshima or Nagasaki. Prewar census figures are unreliable. Though the plutonium bomb was considerably more powerful than the uranium bomb dropped on Hiroshima, the fact that Nagasaki is a city of hills and valleys, and the dropping of the bomb near the secondary target, away from the center of the city, probably means that there were a couple thousand fewer casualties at Nagasaki. Whatever that means. Certainly, people kept dying for decades from the effects of radiation and the heavy metals which were scattered about.
And of course the debate rages on. Did dropping the bomb--dropping two bombs--save a million US casualties in an invasion of the home islands? Was Hiroshima, plus the Soviet entry into the war on August 7, enough? The Japanese high command was in deliberation all that time, with the hardliners holding out for fighting until total destruction, but they were eventually overruled by direct intervention of Hirohito. A message to the Americans regarding impending surrender came through unofficial channels and was discounted.
Was the US intent on dictating the terms of post-war settlement? Did we use the bomb in an attempt to scare the Russians off their designs on Asia and, possibly, Europe as well? Personally I've never given it much consideration; we're not going to change the decision now. In later years Truman seemed to change his story depending on who he was talking to. What can be said is that the military value of the targets was overplayed. Justified or not, we dropped the bomb on civilian populations.
On August 10 the US Army Air Force dropped warning leaflets on the ruins of Nagasaki.