To reiterate: do not read unless you've seen Prometheus.
Skipping over the enigmatic opening prologue for a moment and the unnecessary second "setting-up-the-story" prologue, Prometheus begins with David the Curious Robot. Here, we watch as he wanders aboard Prometheus, a ship traveling across space to a moon where a few scientists have reason to believe it holds answers to the origins of mankind.
While he waits, he studies. He studies Lawrence of Arabia and, by dying his hair to mimic Peter O'Toole's, shows an affinity for the actor and, presumably, the character: a leader from humble beginnings; a charismatic soldier leading a despondent people to overcome their oppressors. He studies language. And he studies the hibernating crew. We get a "flashback" dream sequence with our main scientist: Shaw the Religious. In it, her father describes the afterlife as heaven or a "paradise."
When Prometheus arrives at its destination, the crew is awoken.
We first meet Vickers the Selfish, sweaty and doing push ups... a survivor. We later learn she is David's "sister" or the daughter of trillionaire & bad-make-up-job-old-man Weyland the God, creator of David. Vickers is not a robot like David but acts as such none the less. Her sole motives are selfishness & survival. This is exemplified by the fact that she has her own fully functioning ship within a ship. One that sustains itself and has its own life support so that if the main ship goes to shit, she's got her own escape plan (p.s. she doesn't use it when the time comes). This inner ship also has a psychic mood projection wall. Side note: How the hell and why did it have video of a violin playing girl when Shaw entered it later in the film?
Moving on, David the Curious wakes the rest of the crew. The crew is made up of opposite pairs. There's Vickers the Selfish and Janek the Selfless. Shaw the Religious & her atheist husband Holloway. Two scaredy cat, soon to dead Scientists (one who studies rocks and the other biology). There's also a useless pair who bet on the purpose of the trip... a bet that ends with them choosing to decide the winner in the afterlife because like everyone but Shaw... they're dead now.
Fun fact: the two survivors in the end are also an opposite pair! A human and a robot.
We now learn the purpose of this trip (and again why the second prologue on Earth is completely useless): to respond to the "invitation" left by seemingly all ancient civilizations.
Or, more clearly, to meet mankind's supposed maker: The Engineers.
And so begins the building of a deep mythology while big ideas are thrown around in some pretty clunky dialogue. Holloway, disappointed that The Engineers are "dead," gets drunk and speaks about the clumsy nature of creation.
David the Robot: "Why did you think they made us (robots)?"
Drunk Holloway: "Because we could."
David: "That hurts... Maybe that's why they made you!"
Deep & insightful! Interesting to note that David now has seen Holloway's worldview & Shaw's worldview... wonder who he likes better?
This leads me to the mythology of the Alien universe. And to the opening and closing sequences of Prometheus. Here's how I've pieced together its history:
The opening prologue shows a huge, muscled "human" (a species later thought to be the Engineers) opening a proverbial Pandora's box of what one might consider a powerful biological weapon... a DNA mutator. Let's call it Fire. When ingested or introduced with DNA the Fire destroys and alters it.
In small doses, like that which David gives Holloway, the Fire alters the host's DNA, which slowly & eventually destroys the host itself. During this period between ingestion and death, the host seeks out a reproductive partner in order to create a sort of hybrid offspring, which in turn seeks out its own host to infect... and so on.
The initial Fire ingested by Holloway from David infects Shaw after they have sex. Shaw then removes the subsequent hybrid offspring (in the most unbelievable abortion ever filmed), doesn't kill it and allows it to grow and eventually infect an "Engineer" and thus creating a Xenomorph. The final evolution from "small beginnings."
As Ash puts it in Alien... the Xenomorph is a "perfect organism."
This destruction of the host in the process of creating a new being is the crux of the Alien universe and its ideas of life, death & God. This happens pretty damn often... even Vickers' mini-ship separates from the main ship as it crashes.
Going back to the prologue, the sheer amount of Fire this "Engineer" ingests however, just fucking destroys him. The destruction of DNA happens so quickly, he just dies... no time to infect a host.
I think the "Engineer" might have thought the Fire would give him powers beyond his own. I also believe this "Engineer species" is a war-like one that seeks weapons of mass destruction. I believe they stole the Fire from a more God-like species (seen in the ship over the waterfall). It is this God-like species that Shaw is seeking and will discover in Paradise, the rumored sequel to Prometheus.
Fast forward a few X amount of years and these "Engineers" have harnessed the Fire into a weapon and are currently traveling the universe in little C Ships to destroy other's planets. For what purpose? To conquer? To simply destroy? Whatever the case, it isn't hinted or alluded too in Prometheus (another question for the sequel).
Now, one of these "Engineers" in a C Ship crash lands on LV-246 and thus sets up the events of Alien. A story more or less completely separate from Prometheus. Which is why I think Scott is hesitant to call Prometheus a prequel. The moon that David and Co. land on is the factory where the "Engineers" create, harness and distribute the Fire.
So, back to the current events:
We've got Weyland the Old Man God on board who's somehow speaking to David even though he's all frozen and shit. But, I guess seeing that David can read dreams maybe Weyland is having lucid ones... it's possible... but... yeah... not really...
Through this talk, we discover that Weyland instructs David to infect a crew member in what we can assume is an experiment to see if the Fire is the secret to immortality (whoops!). Being that David seems not to like Holloway too much (and maybe David's attraction to Shaw), Holloway is the lucky subject!
And now, David observes.
Like David, Vickers is an observer but where David instigates, investigates, and presses forward through figuratively and literally opening doors, Vickers observes to survive. In the end, when given the choice to sacrifice herself, she says fuck you and runs like a coward.
Vickers is so selfish and self-preserving, she kills the infected Holloway without any hesitation. In Alien, Ash speaks of the Xenomorph as "a survivor... unclouded by conscience, remorse or delusions of morality." I think Vickers is the rawest form of a human. The part of the DNA that survives beyond the morality and high moral ground of what we consider "humanity" - personified by Janek. She's also an offspring of the "God" of this expedition, Weyland, suggesting that maybe every evolution and offspring is rawer, more chaotic & destructive.
Looking at Janek... he's an artist. A thinker. A musician. A lover. He's also self sacrificing. In the end, he sacrifices himself for the greater good. Not something a Xenomorph would do. Unlike Vickers the Selfish, Janek is selfless. This means that Janek is dead and Vickers is not. Well, if Vickers wasn't so fucking stupid and fucking RUN IN ANY DIRECTION NOT IN THE PATH OF THE FALLING C SHIP...
Moving beyond to the main couple of the film & Lindelof's go to theme: Shaw the Religious & her husband Holloway the Atheist/Scientist. Like LOST, both seek answers to their beginnings but where Shaw continues in her faith that she may meet "God," Holloway believes in more scientific answers. He gives the simple answer to David about a robot's origin, "because we could." This is why he's more easily dismayed by the disappointment of an empty tomb. A man without faith and conviction falls easiest.
Hence the earliest deaths are from the two scientists.
Like LOST, faith & selflessness wins again. Shaw survives. She turns right when the C Ship crashes down on Vickers (who gets the shitty, fuck you death) and she survives the C Ship's final landing by what we'll just say is a little big of deus ex machina.
But what is Prometheus about? Creation through destruction & destruction through curiosity. Like the prologue, the "Engineer" is destroyed by his curiosity. The curiosity of Shaw & Holloway lead them to their eventual destruction, yet through these destructions: creation. Such as the Xenomorph created from the "Engineer" & Shaw's offspring.
I don't think we've met the real Engineers, the pilots of the saucer leaving the waterfall planet in the beginning. However, I have a feeling they look very similar to the elongated skulled Xenomorphs... just not as monstrous looking.
Are their unnecessary points to film... Weyland and his unceremonious death? The "betting" friends? Definitely. Does the film's focus on faith fully pay off? Not really. It's there for a bigger pay off in future films.
I believe that David's attraction to Shaw and her faith is a curiosity. I think it's something that he wants to understand. I think that David needed to get rid of Weyland in order to fully evolve himself. His evolution could not occur without the death of his "God." The only real reason I think Weyland existed in this film in the first place.
I also believe David the Curious will eventually lead a war against the "Engineers."
Which means the haunted house horror of Alien is long gone. The mood and atmospheric nature of this franchise's humble beginnings is long... long gone. This story will become an epic, over-the-top, war saga. Hoping to reach heights and themes of the origins of the universe... a creation so big that it can only bring on a great, great destruction.
All from the simple curiosity of Shaw and her dead husband Holloway.