As the Japanese surrender at the end of WWII, Gen. Fellers is tasked with deciding if Emperor Hirohito will be hanged as a war criminal. Influencing his ruling is his quest to find Aya, an exchange student he met years earlier in the U.S.
In 1937, Japan occupied Nanjing, the Chinese capital. There was a battle and subsequent atrocities against the inhabitants, especially those who took refuge in the International Security Zone.
Japanese troops round up Chinese and Russian prisoners of war and take them to a place called Squadron 731, where they are grotesquely tortured and experimented on to test new biological weapons.