In 1969 during the Vietnam War, jaded MACV-SOG operative Captain Benjamin L. Willard is summoned to I Field Force headquarters in Nha Trang. The officers there tell him that U.S. Army Special Forces Colonel Walter E. Kurtz is waging a brutal war against NVA, Viet Cong, and Khmer Rouge forces without permission from his commanders. He is based at a remote jungle outpost in eastern Cambodia, where he commands American, Montagnard, and local Khmer militia troops. These troops view him as a demigod. Willard is ordered to "terminate Kurtz's command... with extreme prejudice." He joins a U.S. Navy river patrol boat (PBR) commanded by Chief Petty Officer Phillips, with crewmen Lance, "Chef," and "Mr. Clean" to quietly navigate up the Nùng River to Kurtz's outpost.
Before reaching the coastal mouth of the Nùng, they rendezvous with the 1st Squadron, 9th Cavalry Regiment—a helicopter-borne air assault unit of the elite 1st Cavalry Division, commanded by Lieutenant Colonel Bill Kilgore—to discuss safe entry into the river. Kilgore is initially inattentive, as he has not received word about their mission through normal channels. However, he becomes more engaged after discovering that Lance is a well-known surfer. Kilgore, an avid surfer himself, agrees to escort them through the Nùng's Viet Cong-held coastal mouth. The helicopter squadron, playing "Ride of the Valkyries" on loudspeakers, raids at dawn with a napalm strike.
Resisting Kilgore’s attempts to convince Lance to surf with him on the newly conquered beach, Willard gathers the sailors to board the PBR and continue on their mission. Tension arises as Willard insists on the priority of his mission over the Chief's usual patrol objectives.
Slowly making their way upriver, Willard partially reveals his orders to the Chief to convince him that the mission is important and should proceed despite the difficulties they’ve encountered. As Willard studies Kurtz's dossier, he is struck by the mid-career sacrifice Kurtz made by leaving a prestigious Pentagon assignment to join Special Forces, with no prospect of advancing beyond the rank of colonel.
At a remote U.S. Army outpost, Willard and Lance seek information on what is upriver and receive a dispatch bag containing official and personal mail. Unable to find any commanding officer, Willard orders the Chief to continue. Willard learns via the dispatch that another MACV-SOG operative, Special Forces Captain Richard Colby, was sent on an earlier mission identical to Willard's and has since joined Kurtz.
Lance activates a smoke grenade while under the influence of LSD, attracting enemy fire, causing Mr. Clean's death. Further upriver, Chief is impaled by a spear thrown by Montagnards and attempts to kill Willard with the spear point protruding from his chest, but Willard overpowers him.
Willard reveals his mission to Chef, who is now in charge of the PBR. The PBR arrives at Kurtz's outpost, a Khmer temple teeming with Montagnards and strewn with remains of victims. Willard, Chef, and Lance are greeted by an American photojournalist, who praises Kurtz's genius. Willard encounters Colby and two other soldiers among the Montagnards. He sets out with Lance to find Kurtz, leaving Chef with orders to call in an airstrike on the outpost if the two do not return.
In the camp, Willard is bound and brought before Kurtz, after which he is locked in a bamboo cage. One night Kurtz appears and drops Chef's severed head into Willard's lap. Willard is released, and warned not to attempt escape from the camp or he will be shot. Kurtz lectures him on his theories of war, praising the ruthlessness of the Viet Cong. Willard agrees with a lot of Kurtz's ideologies, and deduces he wants to "go out like the soldier" but instead survived multiple traumatic events. Kurtz admits he knows Willard will kill him, and humbly asks him to tell his son the truth of his death.
That night, as the Montagnards ceremonially kill a water buffalo, Willard murders Kurtz with a machete. Everyone in the camp sees Willard departing, carrying a collection of Kurtz's writings, and bow down to him. Willard finds Lance, leads him back to the PBR, and they depart back down the river, away from Kurtz’s outpost. Soldiers on the radio ask if they should carry out with the bombing, Willard chooses not to and turns the radio off.
