The film became notorious in the entertainment press due to its lengthy and troubled production, as documented in Hearts of Darkness: A Filmmaker's Apocalypse. Marlon Brando showed up to the set overweight and Martin Sheen suffered a heart attack. The production was also beset by extreme weather that destroyed several expensive sets. In addition, the release date of the film was delayed several times as Coppola struggled to come up with an ending and to edit the millions of feet of footage that he had shot. The film won the Palme d'Or at Cannes and was nominated for the Academy Award for Best Picture and the Golden Globe Award for Best Motion Picture – Drama.

Act I

The film opens, introducing Captain Benjamin L. Willard (Martin Sheen); a deeply troubled, seasoned special operations veteran. It is 1969. Willard has returned to Saigon from deployment in the field. He drinks excessively and appears to be having difficulty adjusting to life in the rear-area. Two intelligence officers, Lt. General Corman (G. D. Spradlin) and Colonel Lucas (Harrison Ford), and a government man (Jerry Ziesmer) approach him with an assignment: journey up the fictitious Nung River into the remote Cambodian jungle to find Colonel Walter E. Kurtz (Marlon Brando), a member of the US Army Special Forces feared to have gone rogue.

They tell Willard that Kurtz, once considered a model officer and future general, has gone insane and is commanding a legion of his own Montagnard troops deep inside the forest in neutral Cambodia. Their claims are supported by very disturbing radio broadcasts and recordings made by Kurtz himself. Willard is ordered to undertake a mission to find Kurtz and terminate the Colonel's command "with extreme prejudice."

Willard joins the crew of a Navy Patrol Boat, Riverine (PBR), with an eclectic crew composed of: boat commander QMC George "Chief" Phillips (Albert Hall), GM3 Lance B. Johnson (Sam Bottoms), GM3 Tyrone Miller (Laurence Fishburne) a.k.a. "Mr. Clean", and EN3 Jay "Chef" Hicks (Frederic Forrest).

Willard and the PBR crew rendezvous with the 1/9 Air Cavalry, commanded by Lieutenant Colonel Bill Kilgore (Robert Duvall) for transport to the Nung River. He initially refuses their request for transport until Kilgore, a keen surfer, is told by one of his men that Lance Johnson, a professional surfer, is a member of the boat's crew. Kilgore befriends Johnson, and later learns from one of his men that the beach down the coast which marks the opening to the river is perfect for surfing. This changes Kilgore's mind about transporting Willard and the PBR to the river, but from the map there is a Viet Cong-held village at the mouth of the river and Kilgore decides to capture the village. His men advise him that it's "Charlie's point" and heavily fortified. Dismissing this concern with the explanation that "Charlie don't surf!," Kilgore orders his men to saddle up in the morning to capture the town and the beach.

Riding high above the coast in a fleet of Hueys accompanied by OH-6As, Kilgore launches his attack on the beach. The scene, famous for its use of Richard Wagner's "Ride of the Valkyries," ends with the soldiers surfing the barely-secured beach amidst skirmishes between infantry and VC. After helicopters swoop over the village and demolish all visible signs of resistance, a giant napalm strike in the nearby jungle dramatically marks the climax of the battle. Kilgore exults to Willard, "I love the smell of napalm in the morning... The smell, you know that gasoline smell... Smells like, victory" as he recalls a battle in which a hill was bombarded with napalm for over twelve hours.

The lighting and mood darken as the boat navigates upstream and Willard's silent obsession with Kurtz deepens. Incidents on the journey include a run-in with a tiger while Willard and Chef search for mangoes. The boat continues up river and the crew watches a USO show featuring Playboy Bunnies and a centerfold that degenerates into chaos.

Shortly after the Playmate performance, Phillips spots a sampan and orders an inspection over the objections of Willard. Initially reluctant to board the boat, Chef impatiently searches it; a young woman on the boat makes a sudden movement towards a barrel, prompting Clean to open fire and kill nearly everyone on the sampan. As the woman lies dying, Chef discovers that the barrel contains the woman's pet puppy. Phillips insists on taking the woman to receive medical attention; however, Willard ends the debate by shooting her, calmly stating, "I told you not to stop," further alienating himself from the PBR's crew.

Act II