The darkness in Conrad's Heart of Darkness has several meanings, all of which are linked to either the setting (the Belgian Congo), the character of Kurtz, and the tension between civilization and the jungle in which Marlow finds Kurtz.
After arriving in the Congo and finally getting the boat underway to find Kurtz, Marlowe feels himself drawn deeper and deeper into the darkness as the jungle thickens and begins to crowd the boat. The setting itself, then, is part of the darkness.
When Marlowe finally arrives at Kurtz’s station and begins to see the heads of natives on polls, and also realizes Kurtz is actually worshipped by the natives around the station, he begins to realize that Kurtz has abandoned civilization altogether. When Marlowe says, “I saw the inconceivable mystery of a soul that knew no restraint, no faith, and no fear. . . .,” we know that Kurtz has embraced the heart of darkness represented by life in the jungle. In other words, Kurtz’s ties to civilization are gone, and he has become almost the worst example of a native.
Ultimately, Kurtz’s embrace of an “uncivilized” life is Conrad’s way of saying that, when civilization and the darkness come into contact, civilization is not strong enough to win. Kurtz’s last words—“The horror, the horror”—confirms that even he recognizes the negative effects that the jungle had on his personality.