Under The Doors' "This is the End," a helicopter bombs a strip of jungle, which ignites in flames. Dissolve to Captain Benjamin L. Willard, who is drunk and high in a Saigon hotel room. In his voice-over, he says that this is his second tour of duty in Vietnam, and he is waiting for his next assignment. Two soldiers arrive in his hotel room and throw him in the shower to sober him up. Willard is brought to ComSec Intelligence in Nha Trang to be debriefed.
Willard arrives in Nha Trang via helicopter and meets Lt. General Corman and Col. Lucas for lunch. They supply him with information about Col Walter E. Kurtz, who was a celebrated Operations Officer with the 5th Special Forces until he broke away from his assignment and has, by all counts, gone insane. He is currently in Cambodia, having amassed a large local following. Additionally, he ordered the assassination of some South Vietnamese intelligence agents that he was convinced were spies and is now wanted for murder. Willard's mission is to travel up the Nung River and terminate Kurtz's command "with extreme prejudice."
Willard's transport to the Nung River is a Navy patrol boat (AKA a Patrol Boat, River, or PBR). His crew consists of The Chef, Lance, Mr. Clean, and Phillips "The Chief," who captains the boat. They start on their journey, seemingly carefree. While the crew listens to the radio and soaks in the sun, Willard sits quietly in the back of the boat and studies Kurtz's dossier, trying to understand the man's motivations. Soon, the boat crosses paths with the Air Cavalry Division - 1st of the 9th, led by Captain Kilgore. Kilgore is tasked with taking Willard and the PBR to the mouth of the Nung River. The Air Cav is in full-on attack mode, destroying a Vietnamese Village. At first, Kilgore is dismissive but then becomes energized when he hears that Lance Johnson, the famous surfer, is among Willard's crew.
That night, Kilgore hosts a beach party and promises to get the PBR to the mouth of the Nung River, despite the fact that they will have to pass through a Viet Cong stronghold. The next day, the Air Cav airlifts the PBR to its next destination, while Willard and his crew ride along in helicopters. Kilgore likes to play "Ride of the Valkyries" while conducting airstrikes. Kilgore's team successfully destroys the village after calling in a napalm strike, allowing Willard and his crew to continue on their journey.
Back on the boat, Chef gets very stoned and decides to go out into the jungle in search of mangoes. Willard accompanies him, but instead of fruit, they are chased by a tiger. Chef howls madly, "never get out of the boat!" Willard considers Kurtz, who got off the boat and "split from the whole fucking program." He continues reading Kurtz's dossier, and learns that Kurtz had a history of carrying out missions without official clearance, but in the past he had been praised as a hero because Operation Arcangel was a major success. The PBR arrives at Hau Phat where there is a supply warehouse and an upcoming USO show. Willard and his crew are in the bleachers while three American Playboy Playmates dance provocatively for the troops. However, their show is cut short when the over-excited soldiers storm the stage and start pawing at the dancing women. The Playmates are herded into their helicopter and shuttled back home.
The next morning, the PBR moves on up the river towards the Do Lung Bridge. Along the way, Willard continues to pore over Kurtz's dossier. He sees photographs of Kurtz's camp in Cambodia. Everyone - Charlie included - is afraid of Kurtz. Willard comments that the Army has "lost him." Meanwhile, Chief is becoming more concerned about their mystery destination. Willard tells him where they are going - Cambodia. He promises that if Chief can take him as close to the destination as possible, he will let the PBR go back and continue on alone. Later, Willard reads a letter that Kurtz wrote to his son, claiming that the charges against him are insane and accuses the American Army of having "timid morality."
The PBR crosses paths with a Vietnamese sampan, crewed by civilians. According to protocol, Chief makes Chef raid the Sampan to make sure that the sailors are not trafficking supplies to the Viet Cong. A woman onboard won't let him go through her basket, and so Mr. Clean suddenly opens fire and massacres everyone on the sampan. It turns out that the woman, who is still (barely) alive, was only trying to save a puppy, which Lance keeps. Chief wants to take the woman to get help but Willard kills her and tells the crew that they are moving on.
They arrive at the Do Lung Bridge, the last army outpost on the Nung River, at nightfall. Lt. Carson has been waiting for the PBR and delivers an official Army memo to Willard and a bag of mail for the rest of the crew. The outpost is in a state of chaos - every night, Charlie finds a way to blow up the bridge and every day, the Americans rebuild it. Lance, who is tripping on acid, accompanies Willard to shore in an attempt to find the commanding officer - but there is none. They return to the PBR and continue up the river, despite Chief's hesitation.
Willard reads the memo from the Army, which says that Capt. Richard Colby, the last man sent on a mission to find Kurtz, actually defected and has joined Kurtz's followers. Mr. Clean listens to a taped message from his mother when suddenly a cascade of bullets bursts out from the jungle. The crew immediately returns fire, but it's too late - Clean dies with his mother's voice still playing on the tape. Chief bawls over Clean's body. Later, Chef becomes wild with paranoia and Willard claims that Kurtz is close - he can feel his presence. The PBR is attacked again by Kurtz's followers. Willard tries to get his crew not to retaliate, since the arrows are harmless, but they don't listen. A spear pierces Chief through the heart. Before he dies, he uses all his strength to grip Willard's throat, furious as to what he's led them into. Later, Chef and Lance agree to accompany Willard all the way to his final destination.
Finally, the PBR arrives at Kurtz's compound. They are greeted by the Photojournalist, an American civilian who has been documenting Kurtz and his activities. Willard and Lance go on land and see Capt. Colby, who refuses to speak. The steps to the temple where Kurtz lives are covered in human heads. The Photojournalist insists that Kurtz is a great man but that he sometimes just goes too far. Back on the PBR, Chef is scared, calling Kurtz evil and saying he'll do anything to kill the man and get out of there. Willard decides to take Lance with him back to land to find Kurtz, and tells Chef to radio in an airstrike if they are not back by 2200 hours.
On land, Kurtz's followers descend upon Willard and bring him to Kurtz. Kurtz, from the shadows, calls Willard an "errand boy sent by grocery clerks to collect the bill." Later, Willard, showing signs of torture, is imprisoned in a bamboo cage. The Photojournalist tries to convince him that Kurtz is a genius. On the PBR, Chef realizes that it's time to call in the airstrike. At night, Willard is hunched in his cage when Kurtz comes out, standing right by him, face painted in camouflage. He drops Chef's severed head onto Willard's lap.
In the morning, two men carry Willard into Kurtz's quarters, where he stays for days, voluntarily. He claims not to know what he will do and wonders how Kurtz's family and former colleagues would react if they knew how far gone he was. Kurtz tells Willard that he has the right to kill him but not to judge him - they have both witnessed the same horrors in this war. He asks Willard to tell his son the truth about him. Later, when it's dark, Kurtz's followers conduct a ritual sacrifice of a water buffalo while Willard kills Kurtz with a knife. Afterwards, Willard emerges onto the steps of the temple and the crowd kneels before him. Willard, however, drops his knife, takes Lance by the hand, and steers the PBR back down the river. He turns off the radio, buzzing with voices from Trang, and hears Kurtz's last whispered words echoing in his mind: "The horror...the horror."