What did Coppola want to symbolize by the last sequences involving rogue colonel?

In the end of the film, when Willard finally makes it to Kurtz's compound, he discovers that the colonel has gone insane and sees himself as a 'god', lording over the indigenous occupants in that part of the jungle.

In presenting this conclusion, both the novella and the film show that Willard has left one hell for another, the hell of war for the hell of the tortured human psyche.

Kurtz himself has come to terms with the fact that Willard is there to kill him, and in fact he welcomes it, as he knows that he will live on in Willard and eventually make it to the godhood he desires. This is demonstrated when Willard leaves Kurtz's 'hovel' after the killing and drops his weapon, relinquishing his connection to violence, and becoming the new god for the locals.

According to wikipedia:

When Coppola originally organized the ending of the movie, he had two choices. One involved Willard leading Lance by the hand as everyone in Kurtz's base throws down their weapons, and ends with images of Willard's boat pulling away from Kurtz's compound superimposed over the face of a stone idol which then fades into black. Another option showed an air strike being called and the base being blown to bits in a spectacular display, consequently killing everyone left at the base.

The original 1979 70 mm exclusive theatrical release ended with Willard's boat, the stone statue, then fade to black with no credits, save for '"Copyright 1979 Omni Zoetrope"' right after the film ends.

This has prompted many to speculate that the intense napalming seen when the film starts is actually the destruction of Kurtz's compound, a flash-forward if you will.

I'm sure there are many more eloquent essays written about this subject, but I hope I've provided a good starting point for you.

The greatest movie of all, and the least understood. The theme of the movie is this: THROUGH THE EYES OF THE INSANE, A SANE MAN APPEARS TO BE CRAZY.

To understand that theme, you must realize that the viewer's perspective is that of the insane. We are seeing things as the insane sees them. Secondly, you must understand the setting: The U.S. failed in Vietnam because it was unable to fully commit to war in Vietnam. In the actual war, the U.S. won virtually every battle, but failed to accomplish anything and ultimately pulled all of its troops out of the country. That is an amazing thing if you think about it - to win all the battles, but lose the war.

Why did that happen? Because the U.S. was confused, did not have a clear objective and was even in coflict with itself. If you think of the U.S. as a nation, you might say, well "that's politics." But what about a person who was "confused, did not have any clear objective, and was in conflict with himself? Would you not call him insane?

In the movie, the Air Cavalry Colonel who loved the smell of napalm in the morning accurately demonstrates both how capable America was of winning any battle in Vietnam and how winning those battles accomplished nothing, BECAUSE America's objectives were confused, undefined, and meaningless (insane). The air Cav Colonel fought and won a battle, very effectively, so that he could go SURFING (insane). He had no sane objective, no concern for whether the war was won or lost, and no regard for the horror of war (insane).

Kurtz, always regarded in the movie as the one man who DID understand how to win (Precise goals and strength to endure the horror of war) was restrained by his superiors and not allowed to win - because they had the insane notion of fighting an 'ethical war' Dropping bombs on people wasn't horrific to them, but curse words were (insane). Kurtz was NOT actually insane. The Air Cav Colonel WAS insane, as was everyone else.

Kurtz tried and tried and tried to reach Captain Willard and show him who actually WAS insane. Willard realized the truth, but chose to kill Kurtz and remain in the insane world rather than being outcast.

• The BEAUTY of Apocalypse Now: In an insane world, being sane is crazy.
• The unparalleled GREATNESS of Apocalypse Now: We DO live in an insane world, Coppola is trying to explain that, but all the insane people just think he's crazy.

By "the ending" of this film, we can either refer to sheen's departure from the compound or the airstrike credit sequence. Frankly, both are ambiguous, an essential ingredients to any cult film [cf "bodysnatchers"] that said, it seems fairly clear that sheen, having killed brando, has assumed the identity and im/morals of the latter. He has become that which he seeks to destroy etc. As far as i can tell, the airstrike sequence was added, being spare footage but too valuable to waste (wastage was high on the project). It does however, suggest a futility to the entire Vietnam war , indeed the "apocalypse" project itself, and is in its way quite excellent.