The film follows a river journey from South Vietnam into Cambodia undertaken by Captain Willard (Martin Sheen), who is on a secret mission to assassinate Colonel Kurtz (Marlon Brando), a renegade Special Forces officer who is accused of murder and presumed insane.

The film is a metaphor for a journey into the self and shows how the self, in the face of war, darkens beyond recognition. As they move upriver, Willard and the PBR crew become more agitated and separated from reality. Each experiences his own kind of mental breakdown.