Story 1: Mankind creates God. The Machine is their object of worship. It is their usher into the future, and they cannot control it. Everyone with power tries to fit it into their mold and make it what they want it to be, and it destroys them. Nothing but destruction results from their desire for power and control, and their "god" makes sure of it.
Story 2: God creates Mankind. The loving, benevolent scientist creates 9 life forms, and dies so that they might live. He breathes his own life into them, and charges them with the salvation of the world. Sound familiar? Here, mankind is searching for their creator. They are searching for the answers to the "Big Questions" that every philosopher is familiar with: "Who are we, Where did we come from, and Where are we going?" So in both stories, we have God and we have man.
In one case, God creates creatures in his own image, and everything it touches reeks with malice. The protagonists spend their lives trying to destroy it, reasoning that the world would be a better place without it. This is a picture of the relationship between God and the unsaved world. They acknowledge him, but they hate him.
In the second case, God creates creatures in his own image, and here's where another separation is revealed: One is fearful and cowardly. Two, Three and Four seek knowledge and understanding. Five knows to do good but isn't sure how. Six sees the full picture, but is disregarded as a lunatic. Seven is bold and willing to fight all that challenge her. Eight is big and dumb, following orders and hitting really really hard. Then you have Nine, who is the summary of all of these. He is the balance between the rest. This goes to show that even a good God will give his creation freedom to become what they will.
But all this is just to set the stage. At the end of the movie, there are two significant elements which we are left to ponder: Both Gods are dead. The Scientist died to preserve life, and the Machine died trying to take it away. But in the end, we are still faced with a world without God. The second point to note here is that only three human traits are represented in the survivors: courage, balance, and the pursuit of wisdom. All the other archetypes represent the exact same mentalities found in the people who created the Machine and destroyed the world.
So, in the last scene, we are left what appears to be the true model for humanity living in a world without God, and the quote "It's our world now; it is what we make of it."
And herein lies the purest form of true existentialism in its entirety.
