Apocalypse Now is essentially the short story
Heart of Darkness at the end of both the protagonist(Willard) becomes the "god" that the antagonist(Kurtz) was.Only Willard chooses to destroy what Kurtz has created he still leaves a part of himself behind (like metaphysically
). So at the end there Willard says something to the effect of "I was not in their Army anymore" he is saying that he is no longer part of that system that way of things.
You really have to watch Apocalypse a few times to get every detail.For example I bet you did not notice that Colby(the previous SF man sent to kill Kurtz) did not kill himself he converted to follow Kurtz.
The French rubber plantation in Cambodia where they bury Clean? That symbolizes how we cling to war even when the gig is up.The French where in Indochina(Vietnam,Laos,Cambodia) before the US was and they lost yet here you see these hardcore Frenchmen clinging to an utterly lost cause(by about 14 years).
Kilgore is just as insane as Kurtz.
This web page explains it well
http://home.roadrunner.com/~jhartzog...tzwillard.html
Here is another pretty good analysis
http://www.fastenupyourseatbelts.com...wAnalysis.html
It is a rather complex film(compared to the typical action flick).