The film is a graphic depiction of the war atrocities committed by the Japanese at Unit 731, the secret biological weapons experimentation unit of the Imperial Japanese Army during World War II. The film details the various cruel medical experiments Unit 731 inflicted upon the Chinese and Soviet prisoners at the tail-end of the war.

In the spring of 1945, Japan established a secret base, Unit 731 in Manchuria, where many innocent Chinese, Korean and Mongolian people were killed in grotesque experiments. An idealistic young doctor , Morishima, is horrified by the experiments being performed in the camp and when his fiancée arrives disguised as a Chinese prisoner he sets out to liberate the camp. A docudrama sequel to the notorious Men Behind the Sun, which pulls no punches when it comes to delivering the shocks!

Black Sun: The Nanking Massacre depicts the brutal events behind the Nanking Massacre committed by the Imperial Japanese army against the Chinese people during the Second Sino-Japanese War.

During the shut down and destruction of the Japanese test camp Squadron 731 in Manchuria, a soldier becomes infected with a virus developed during the camp's testing and risks spreading it into Japan on the train ride home.