Apocalypse Now opens in Saigon in 1968. Army captain and special intelligence agent Benjamin Willard is holed up in a hotel room, heavily intoxicated and desperate to get back into action. He has completed one tour of duty in Vietnam, only to go home a changed man, miserable amid the confines of civilization. After agreeing to a divorce, he has returned to Vietnam for a second tour and now waits restlessly for a mission.

Two officers arrive to escort Willard to Nha Trang, where he meets with two military superiors and a CIA operative, who brief him on a rogue Green Beret colonel named Walter E. Kurtz. Willard is ordered to find and “terminate” Kurtz, who has become unhinged and committed murder with the help of a native Montagnard army. Kurtz currently is stationed at an outpost in Cambodia with the Montagnards, who treat him as a god. Kurtz is insane, the officers say, and his methods are “unsound.”

To reach Kurtz, Willard joins the crew of a Navy river patrol boat (abbreviated PBR, as in Patrol Boat River), who are to ferry him up the (fictional) Nung River to Cambodia. The boat’s crew consists of four men: Chief, Chef, Lance, and Clean. With Willard on board, the crew makes its rendezvous with the Ninth Air Cavalry, who are to escort the PBR to the mouth of the river. The crew members find themselves in the middle of a B–52 bomber strike. Willard encounters the cavalry’s commanding officer, Lieutenant Colonel Bill Kilgore, who assures Willard his cavalry will set the PBR safely at the mouth of the river.

At dawn, Kilgore orders an air attack on a Vietcong-controlled village, and one of the film’s most memorable sequences begins. The helicopters approach, blasting Wagner’s “Ride of the Valkyries” through loudspeakers as the villagers scatter. During the intense air strike, a chopper plunks the PBR down in the river successfully. From this point on, Willard and the crew embark on a journey consisting of a number of episodic encounters connected by Willard’s narration.

The first episode takes place in the jungle. Chef’s craving for mangoes leads him and Willard to disembark and explore the jungle. Amid mammoth trees and dense vegetation, a tiger lunges out at them from the shadows. Chef and Willard run back to the boat. Chef has a nervous breakdown as the rest of the crew shoots blindly at the jungle, assuming the danger is Vietcong. Chef’s breakdown darkens the crew’s mood.

Further up the river, the crew meets a U.S. base supply depot. They dock and collect fuel, cigarettes, and other supplies, then join the throng of men in an amphitheater that has been erected by the river. Soon, a helicopter arrives and drops three Playboy Playmates onto the stage to perform in a USO (United Service Organization) show. The Playmates perform to Flash Cadillac’s song “Suzie Q” and taunt the sex-starved troops with seductive shimmies and bump-and-grind moves. When some of the soldiers run onto stage in a frenzy, the show is cut short and the Playmates are quickly evacuated.

The crew returns to the PBR, and the boat soon meets other patrol boats coming in the opposite direction, with whom they engage in mock warfare. As the crew continues on and tempers flare up more frequently, Willard obsessively reviews Kurtz’s dossier. Lance and Chef are continually under the influence of drugs, and Lance in particular becomes withdrawn, smearing his face with camouflage paint and saying little.

One day, Chief insists on stopping a sampan (a small boat) carrying several Vietnamese peasants and supplies downriver. At Chief’s command, Chef boards the sampan and searches it. Chief orders Chef to look inside a rusty yellow can that a peasant woman on the sampan was sitting on; when Chef does, the woman makes a sudden move toward the can. Clean starts shooting at random, killing all the civilians on board except the woman. Once the shooting subsides, Chef looks inside the can and finds only a small puppy. Noticing the woman is still alive, Chief orders Chef to bring her on board, saying the crew will take her to a “friendly” hospital nearby. Willard steps forward, points his gun at the woman’s chest, and fires, killing her so that his mission can proceed without a detour. The rest of the crew begins to see him in a different light.

Continuing upriver, the shaken crew reaches an army outpost under fire in a gunfight for an American-held bridge—the last military outpost before the Cambodian border. Willard is unable to find a commanding officer onshore but is given a packet of mail for the boat. One of the letters in the packet informs Willard that the U.S. military previously sent another man on the same mission to retrieve Kurtz but that the man is now operating with Kurtz. As Clean listens to an audiotape letter from his mother, the PBR comes under a surprise attack by Vietcong, and Clean is shot fatally.

The boat continues upriver, only to meet another surprise attack. Primitive natives onshore shoot a storm of arrows at the PBR. Chief is impaled with a spear and dies. With two men gone, the survivors at last reach Kurtz’s camp, a macabre site in which countless dead bodies and severed heads are strewn about seemingly at random. A hyperactive American photojournalist, unabashed in his worship of Kurtz, greets the boat.

Willard and Lance disembark to find Kurtz, leaving Chef with instructions to call in an air strike if they are not back at the boat by a specified time. The natives under Kurtz’s control drag Willard through the mud and grant him an audience with Kurtz, who imprisons Willard in a cramped tiger cage. During the night, Kurtz throws Chef’s severed head into Willard’s lap. Willard is freed the next day and given freedom to roam Kurtz’s compound. He listens to Kurtz’s philosophizing for several days.

In split scenes, Kurtz’s natives perform a ritual sacrifice of a caribou, while the film intercuts with images of Willard emerging from the river and approaching Kurtz’s quarters. As the caribou is ritualistically slaughtered, Willard slaughters Kurtz with a machete. Kurtz’s last words are “the horror, the horror.” When Willard emerges, the natives acknowledge him as their new leader and god. He throws down his machete, finds Lance amidst the Montagnard, and returns to the boat. Willard shuts off the radio, and he and Lance pull away from shore as rain begins to fall. Kurtz’s last words are echoed again as the film fades to black.