Black Rain portrays the aftermath of the atomic bomb attack on the Japanese city of Hiroshima. The bomb and the radiation it creates become clear symbols of the power of atomic energy. A new and unknown weapon falls on an unprepared city, and the inhabitants of the city try to save themselves and their loved ones, unaware of the radiation that now lingers over Hiroshima. The ruined city, the massive mushroom cloud, and the titular black rain are all extensions of the atomic bomb as a symbol of death and destruction. While the characters are familiar with the air raids and the incendiary bombs the Americans have previously dropped on Japan (to the extent they have received training and understand how to protect against such weapons), they do not know how to deal with the new weapon. The atomic bomb symbolizes death because it is so unknown and so unlike anything that has come before.

The strange and inexplicable nature of the bomb symbolizes the extent to which August 6 is a clear division between the past and present in Japanese society. The society that existed before the arrival of the atomic bomb ceases to exist, and like the radiation scattered across the city, the new society that emerges will be imbued with poison and trauma that many of the victims do not see or understand.