Two main reasons
First, Geography, Hiroshima was a flat open space, the blast was on target and spread out well. Nagasaki is located in a valley that the blast wasn’t’ as impactful
Second, aiming… they pilots probably missed their target on Nagasaki because of bad weather and feeling forced to drop the bomb. They claimed everything was fine with weather (historians aren’t so confident) … but they probably missed their target and hit a poorer location, so the bomb wasn’t as effective due to the geography of Nagasaki being in a valley
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