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Nagasaki's fate was sealed in a last-minute decision by Secretary of
War Henry Stimson.
Before Stimson's intervention, the port city was not even on the original
list of cities targeted for the atomic bomb. And it made the list only as
a backup site.
In May 1945, Manhattan Project officials set up a committee to pick the
best targets.
The committee examined the range of a fully loaded B-29, identified cities
undamaged enough to serve as a measure of the bomb's destruction, examined
weather conditions and considered the military value of potential targets.
By late July, the group had a list of four cities:
n Kokura, which had one of Japan's largest munitions plants.
n Hiroshima, a major staging area for Japan's army and navy and the site
of several industrial plants.
n Niigata, a major port on the Sea of Japan with an oil refinery, a tanker
terminal and an iron works.
n Kyoto, the former capital of Japan, a major industrial city with plants
producing parts for machinery, aircraft and artillery.
Stimson wanted Kyoto off the list because of its religious and historical
significance to Japan.
Gen. Leslie Groves, head of the Manhattan Project, wanted Kyoto to remain
on the list because he believed it was a legitimate military target, and
because its huge size made it a good gauge for the effects of an atomic
blast.
Stimson overruled Groves, and Nagasaki was added in Kyoto's place.
Few details are available on how Nagasaki was picked, but the city contained
two arms factories, a steel works and the massive Mitsubishi shipyards.
One factory made some of the torpedoes used on Pearl Harbor.
Richard Rhodes' The Making Of the Atomic Bomb speculates that because Nagasaki
was on the opposite side of a Kyushu mountain range from Kokura, military
planners thought even if one city was fogged in, the other was likely to
be clear.
Also, Nagasaki had not been bombed much - which meant the Allies could accurately
measure the scope of the destruction.
For the first mission, Hiroshima would be the primary target, Kokura would
be the second choice and Nagasaki the third.
On the second mission, Kokura would be the target, and Nagasaki would be
the backup. Niigata was too far away to be a practical third choice.