4 months before August 1945, Tokyo had already been reduced to a smoldering ruin for all intents and purposes.

Operation MEETINGHOUSE, on March 9, 1945 involved over 300 B-29's using primarily incendiary bombs on the city, where the majority of buildings were very flammable. The result was almost 1/3 of the city was gone entirely, and most estimates place the death toll at between 100k and 150k with some up to 200k dead. That would mean based on various estimates the one raid killed more than both the Atomic bombings combined. That was the largest raid, but far from the only, from about November 1944 onwards to the end of the war, large B-29 raids regularly visited the city. Thus when the targeting committee began looking at targets to use the bombs on they ruled Tokyo out fairly early as the destructive power of it would be less obvious when used on a city so thoroughly bombed already.

The initial proposal for selection in May required targets that:

• Were "important targets in a large urban area of more than three miles in diameter"
• Were "capable of being damaged effectively by a blast"
• Were "unlikely to be attacked by August."

The initial targets selected and given grades were:

• Kyoto (AA)
• Hiroshima (AA)
• Yokohama (A)
• Kokura Arsenal (A)
• Niigata (B) The Imperial Palace was explicitly discussed and rejected by the committee. It wasn't considered a war important target. It could be damaged, but the topography wasn't conducive to making an particularly effective demonstration. And it clearly was going to be attacked before August. In fact it already had been before the selection committee met. While the Palace had largely been avoided during Operation Meetinghouse, it had taken some errant bombs. And the area three miles diameter around the Palace was devastated. The committee did however recommend that the Palace be further studied for potential inclusion on the list. They were aware of the potential psychological effects leveling the palace could have.

After this initial list was created, it was regularly adjusted. Kyoto was famously removed to preserve its cultural treasures. And other cities like Nagasaki were added. This was a result of additional criteria being added, including emphasizing cities that would be a shorter run for the bombers, making cities along the Southwest coast more attractive.