I have often thought that it was proving the existence of a god. See, Frank(He is manipulated dead) is god, or at least his voice, guiding Darko into what he must do to save the universe. The others are the manipulated living, they are there to hint Darko in the right direction. Its why Grandma Death went to check her mail, it wasn't because she wanted to have someone write, no, it was so some would say "Someone needs to write her." (Movie quote, "Someone need to write that *****") The spears that Donnie sees are the determined path created by said god, this allows him to see into the future and see what he must do exactly. Gretchen is the want, without her, Donnie would have no want to save the world. She is the reason Darko kills himself, he is protecting her, and also everyone else. Donnie is also blessed with rather odd powers, this is a sign that god has blessed him. Its why when he asks Frank, "Why do you wear that stupid bunny suit?" Frank replies, "Why do you wear that stupid human suit?" because Darko knows he is more than human now. This is a very deep movie, and its not supposed to be taken as a Christian movie either, judging by all the unmoral things Darko does in the movie. But I am hard pressed to see how this movie would make sense other than saying it is trying to prove the existence of a god using a very scientific idea.