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They were not targeted specifically. An initial list of 6 target cities was prepared in May 1945, they were just 2 of the cities on this list. Along with this list orders were prepared to "use the atomic bombs as they become available". No other authorization to use the atomic bombs was required, they would just continue being used until the president canceled these orders.

When the 509th Composite Group arrived on Tinian in July 1945, they did periodic practice bombing missions on various Japanese cities not included on the list using 10000 pound "pumpkin bombs" filled with Composition B and fused to explode on impact. Each of these missions used 3 B-29s just like the real atomic bombing missions would: one plane carrying the bomb and two observation planes.

For the real missions the field commanders of the 509th selected 3 cities from the list: a primary target, a secondary target, and a tertiary target. The real atomic bombs were RADAR altimeter fused to explode at an altitude calculated to maximize the area of blastwave damage.

The Little Boy MK-I atomic bomb became available (assembled and checked out) on the morning of August 6, 1945 and the 3 planes took off from Tinian. This bomb was successfully used on its primary target Hiroshima.

The Fatman MK-III atomic bomb became available (assembled and checked out) on the morning of August 9, 1945 and the 3 planes took off from Tinian. Due to problems one of the observation planes did not meet up with the plane carrying the bomb and the other observation plane. Two planes continued on to the primary target Kokura, but after finding it obscured by smoke from a nearby city that had been firebombed the night before it was decided to proceed to the secondary target. This bomb was successfully used on its secondary target Nagasaki despite heavy cloud cover, but the bomber was very low on fuel by that time and could not have made it to the tertiary target if they had not been able to use their bomb on Nagasaki.

Another MK-III atomic bomb had been readied by Los Alamos by this time and shipped to San Francisco from which it would have been flown to Tinian and become available (assembled and checked out) sometime in late August 1945. It would have very likely been used on Kokura (but actual final selection of the 3 cities would still have been made by the field commanders). However before it arrived in San Francisco the Japanese had indicated they would surrender and Truman ordered the bombing of Japan stopped, so it was returned to Los Alamos (probably becoming the first atomic bomb in the US stockpile).

The Manhattan Project was prepared to manufacture and "make available" 20 more MK-III atomic bombs for use on Japan before the end of 1945.

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Q: Why did the US target Hiroshima and Nagasaki to drop the atomic bombs?
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