Tokyo had already been pummeled by the 8th Air Force earlier in the year. In March 1945, Operation Meetinghouse sent 330 B-29s over the city at low level, dropping incendiary bombs. This attack alone killed roughly 100,000 people, more than in either the Nagasaki or Hiroshima bombings.

/u/Restricteddata is the resident expert, and he has a pretty good blog post here that talks about Tokyo and atomic weapons.