Why didn't the US choose to demolish Tokyo with an atom bomb?

Question

Tokyo was Japan's capital. Why didn't the US choose Tokyo to demolish with Atom Bomb? **Bonus Question:** What factors decided to bring Hiroshima and Nagasaki on table?

Answer 1

Earlier in the year Tokyo had been hit by several devastating fire bombing raids that had effectively leveled most of the city. Hiroshima and Nagasaki were chosen as they were largely left in tact from any major bombing operations and had several strategic targets located in the two cities, including but not limited to; major military bases, factories, transportation hubs, shipyards and military headquarters. Nagasaki was actually the secondary target as the original target was Kokura but the city was covered by clouds.

Answer 2

Likely for the same reason a proposal to drop the first on Mt. Fuji was also rejected - targeting something important to the population as a whole possibly could have stiffened their resolve instead to making capitulation more likely. The air defense of Tokyo was also probably much stiffer. Also, purely from a war standpoint, I suspect those two cities likely had more factories, drydocks and such vital to the Japanese war effort.