Marlow is portrayed by the character Willard (Martin Sheen) who is sent on a top secret mission to assassinate a Colonel Kurtz (Marlon Brando) who has defected from all army operations and is running his own show, so to speak, up a river deep in the jungles of Cambodia. So begins the dark journey as Willard, through reading files on Kurtz, becomes more and more obsessed with the man, and less concerned with the mission to kill him.
Upon meeting, Kurtz explains to Willard a story in which his unit had been sent to innoculate the children in a small village. Upon returning, Kurtz found the entire village destroyed by the enemy, and with it amongst the rubble a pile of "tiny innoculated arms". He explains, "It hit me. It hit me in the forehead like a diamond bullet. The strength! The strength it took for normal moral men to do something like that! If I had ten divisions of such men, our troubles here would be over very shortly."
Like the Kurtz in Heart of Darkness, Colonel Kurtz has discovered a way to perform his duties perfectly through sheer brutality. The moral dilema has already been negated by the fact that terrible things are being done to the same people by the same army that finds Kurtz's methods "unsound". He was doing just what he was supposed to do and that was win. The idea Coppola is portraying in this film is that nothing about that war was justified. It was a brutal slaughter without reason, and all petty attempts at making it look humane were the lies of generals and politicians watching over the war from the outside, trying to keep their images clean in public view.
Another aspect of this movie that was interesting is that it seems almost as if Willard goes through a much stronger transformation than Marlow does, not only seeing eye to eye with but becoming a Kurtz-like character as brutally chops him to bits with a large knife.
This is one of the greatest films of all time. I'd recommend it to anyone. It's especially interesting after having read Heart of Darkness. Just set aside about four hours, rent the Redux, turn out the lights, and get ready for some real darkness.