Willard reads a letter from Col. Kurtz to his son that reveals his hatred of the system that once extolled him. Col. Kurtz explains that while the Army has accused him of murdering the four Vietnamese double agents, the charges are, "in the circumstances of this conflict, quite completely insane." He continues:
"In a war, there are many moments for compassion and tender action. There are many moments for ruthless action. What is often called "ruthless" . . . may, in many circumstances, be only clarity: Seeing clearly what there is to be done and dong it — directly, quickly, looking at it."
Col. Kurtz feels that in murdering the double agents, he was simply exhibiting a soldier's "clarity": The agents were captured, they were enemies, and were therefore killed. What Kurtz detests is the Army's purposeful lack of "clarity": He knows that they cannot (in this war) afford to appear "ruthless" and are therefore attempting to smear his name and color his actions as insane. Col. Kurtz ends his letter with an expression of his hatred of lies: "As for the charges against me, I am unconcerned; I am above their timid, lying morality and so I am beyond caring." Later, Col. Kurtz remarks, "We train young men to drop fire on people but will not allow them to write 'fuck' on their airplanes, because it's 'obscene.'" This hypocrisy enrages Kurtz to the point where he can no longer abide by the "timid" moral guidelines of the Army, just as Conrad's Kurtz can no longer abide by the "methods" suggested to him by the Company. Both men detest the lies of their superiors: Recall Kurtz's remark to the Manager when he arrives at the Inner Station to "rescue" him: "Save me! — save the ivory, you mean. Don't tell me. Save me!" His subsequent remark to the Manager about his health ("Not so sick as you'd like to believe") is the equivalent of Col. Kurtz's letter: Both the Company and Army want to pretend that their "Kurtzes" are insane rather than admit the truth, which is that both men see their respective organizations for what they truly are.
When Willard meets Kurtz in the last part of the film, Coppola stresses Kurtz's power — but also the weariness that this power has created in Kurtz. Willard is taken prisoner and kept in a cage; on a rainy night, Willard is awakened by Kurtz, who drops the head of one of Willard's crew in his lap, as if to say, "This is what I am capable of doing on a whim." After this show of force, however, Kurtz begins nursing Willard back to health, and Coppola eventually makes clear the idea that Kurtz knows Willard's mission and — more importantly — wants him to carry it out. "If I was still alive it was only because he wanted it that way," Willard remarks. Like Kurtz in Heart of Darkness, Col. Kurtz cannot sustain his life of exhausting emptiness. Both Kurtzes succumb to the temptation of "forgotten and brutal instincts" — and both find that their lives become "hollow" as a result. As he approaches Col. Kurtz with a machete, Willard's voice-over explains, "Everyone wanted me to do it," including the jungle, "Which is who he really took his orders from." Col. Kurtz wants to die, because after learning what he did about himself, he needs (as Willard explains), "Someone to take the pain away." When Willard kills him, Col. Kurtz offers little resistance; Coppola intersperses the scene of Col. Kurtz's murder with the sacrifice of a bull to suggest that Col. Kurtz is "sacrificed" for the sins of the Army. Eventually, he speaks the same final words as his counterpart with the same ambiguous effect.
After Willard kills Col. Kurtz, he leaves the hut, machete in hand, and sees hundreds of Kurtz's followers bow to him as he walks to his boat. Before he begins his return, however, Willard hesitates, for he has the chance to become Kurtz's successor. After a moment, however, he returns to the boat and the small amount of safety it provides. Thus, in both Heart of Darkness and Apocalypse Now, both protagonists learn the same lesson: Even a man as "enlightened" and revered as Kurtz can succumb to his dark side if he is freed from the restraints of society. Both protagonists are also able to retreat from the fate that awaited Kurtz — but both of them also come face-to-face with "an impenetrable darkness" that challenges their most basic moral beliefs. Without having met their respective Kurtzes, both men would have found the world less dark than they do at the time of their narrations. But as both Conrad and Coppola suggest, one cannot "unsee" what he has already glimpsed — Marlow and Willard can pull back their feet, but will never forget what lay over the edge.