In 1970, during the Vietnam War, U.S. Army Captain and special operations veteran Benjamin L. Willard (Martin Sheen) is offered an assignment to follow the Nung River into the remote jungle, and find rogue Special Forces Colonel Walter E. Kurtz (Marlon Brando). Kurtz apparently went insane and now commands his own Montagnard troops inside neutral Cambodia as a demi-god. Willard is told his objective is to infiltrate the Colonel's team and to terminate the Colonel's command "...with extreme prejudice".
Ambivalent about the mission, Willard joins a Navy PBR commanded by "Chief" (Albert Hall) and crewmen Lance (Sam Bottoms), "Chef" (Frederic Forrest) and "Mr. Clean" (Laurence Fishburne) to head upriver. They rendezvous with brazen Lieutenant Colonel Bill Kilgore (Robert Duvall), a commander of an attack helicopter squadron, to discuss going up the Nung river. Kilgore initially scoffs at them, but befriends Lance, both being keen surfers, and agrees to escort them through the Viet Cong-held coastal mouth of the river due to the surfing conditions there. At dawn the helicopter raid commences. Amid the attack Kilgore calls in a napalm sortie on the local cadres and the rivermouth is taken. Willard gathers his men to the PBR, transported via helicopter, and begins the journey upriver.
Tension arises between Chief and Willard as Willard believes himself to be in command of the PBR, while Chief prioritizes other objectives over Willard's secret mission. Slowly making their way upriver, Willard reveals part of his mission to the Chief to assuage the Chief's concerns about why his mission should take precedence. As night falls, the PBR reaches the chaos of the last US outpost on the Nùng river, the Do Long bridge. Seeking some intel on what's upriver, Willard and Lance proceed through the base seeking information. Finding no info, and disgusted, Willard orders the Chief to continue upriver as an unseen enemy launches a strike on the bridge.
The next day, Willard learns from the dispatch that another Special Operations Group (SOG) operative, Captain Colby (Scott Glenn), who was sent on an earlier mission identical to Willard's, is now listed as missing in action. Meanwhile, as the rest of the crew read letters from home, Lance pops open a purple smoke grenade for fun. This catches the attention of an unseen enemy in the trees and the boat is fired upon, killing Mr. Clean. Later, in a separate attack, Chief is killed.
Eventually the PBR arrives at Kurtz's outpost and the remaining crew members are met by an American freelance photographer (Dennis Hopper), who manically praises Kurtz's genius. As they wander through the compound they come across Colby, who stands nearly catatonic along with other US servicemen, now serving in Kurtz's renegade army. After returning to the PBR, Willard later takes Lance with him to the village, leaving Chef behind with orders to call an airstrike on the village if they do not return.
In the camp, Willard is subdued, bound and brought before Kurtz (Marlon Brando) in the darkened temple. Tortured and imprisoned, Willard screams helplessly as Kurtz drops Chef's severed head into his lap, meaning there will be no airstrike. After several days, Willard is released and given the freedom of the compound. Kurtz lectures him on his theories of war, humanity and civilization while praising the ruthlessness and dedication of the Viet Cong. Kurtz discusses his family and asks that Willard tell his son "the truth" about him in the event of his "death".
That night, as the villagers ceremonially slaughter a water buffalo, Willard stealthily enters Kurtz's chamber as Kurtz is making a tape recording, and attacks him with a machete. Lying mortally wounded on the ground, Kurtz, with his dying breath, whispers "...The horror... the horror...". The villagers are now abuzz about something amiss in Kurtz's quarters, and seeing Willard departing the rooms with bloody machete in hand, they bow down and allow Willard to take Lance by the hand and lead him to the boat. The two of them ride away as Kurtz's final words echo eerily as the world fades to black.