The Prometheus is taken out by a Heroic Sacrifice: ramming itself into the Space Jockey ship and creating a massive explosion. Prometheus gave fire back to the gods, with interest.
David's yellow visor helmet appears to allow him to see into the dreams of people in stasis (or he wouldn't have worn it when watching Shaw's dreams). It also allows him to communicate with an in-stasis Weyland Sr.
The unusual, overly predatory, and even self destructive nature of the iconic Xenomorphs is finally explained. They never evolved in the wild through evolution but were engineered by the space jockeys as a perfect WMD. They can spawn from a single egg or possibly even a few cells. They rapidly gain momentum once people are being infected. They instill paralyzing terror. They keep going until they run out of things to kill. And once the planet is purged of all life and the active Xenomorphs starve to death, the eggs stay behind for thousands of years making sure the few survivors can't repopulate. And on top of that, the engineers have an arsenal of other biological nasties at the ready in case all of this wasn't enough.
The Engineer at the beginning is Prometheus... or at least a metaphorical representation of Prometheus; a wayward "god" who created a new sentient species, possibly against the wishes of the other "gods" who intend to correct his mistake.
Here's for hoping that this film's financial success will bring that movie back up as a competing franchise.
The Black Liquid in this film also gives an answer as to another mystery of the Alien Universe. Namely the deleted scene in the first Alien Movie where a lone Xenomorph was shown to be mutating captured crewmen into either eggs or new Xenomorphs. This makes a HELL of a lot more sense given the fact that we now know the Xenomorph was almost certainly created using the Black Liquid Mutagen, and may well be able to replicate it's properties to some degree in order to spread.
When Shaw tries to use the pod in Vicker's chamber to abort the alien fetus growing inside her, it says that it is programmed only for male surgeries. One may briefly wonder why Vickers would have a male pod, until you realize that her aging, sickly father is also on the ship, and may need some emergency medical assistance when he comes out of cryo-sleep.
The weird little glance down Vickers does when the hologram of Weyland mentions how David is like the son he never had makes more sense once you find out that she's his daughter.
To expand upon this, many posters on /tv/ were annoyed at the Vickers slept with the Janek for no apparent reason than to leave the stranded scientists unmonitored. I realized on second viewing, that in actuality, her Daddy Issues are triggered when she is accused of being a robot: she resents David for the attention Weyland gives him and rebels with promiscuity.-th0114nd
Nah Vickers is probably an android. She makes a comment early on about being a very cautious person - but later we find out that she didn't even bother to have the medical pod programmed for female anatomy. She probably slept with Janek to throw off his flippant accusation about her being a robot. The emphasis she places on the word father could have been sarcasm rather than anger.
If Vickers is an android, it explains why she recovers from stasis almost instantly while the rest of the crew is left nauseous and weakened.
Why would a replicant need to do pushups?
To have an excuse for showing Charlize Theron in a skimpy outfit?
If any knowledge of the Engineers' language ever got back to Weyland(-Yutani), there is now a plausible explanation for Mother deciphering the distress call in Alien.
The normal Xenomorph lifecycle is depicted in reverse. It starts with the infected Holloway accidentally causing a proto-chestburster to grow inside Shaw. The proto-chestburster grows into a proto-facehugger and implants an egg into the Engineer, which erupts as a proto-Xenomorph.
Fridge Horror, actually — the thing in Shaw wouldn't need to burst out her chest. It already had an exit.
Yes, we know, when she cut open her —oh. You mean. Oh.Oh.
Is that really any worse than smashing through a wall of organs, muscle and bone in a "standard" chestburst?
Consider this: if a host actually survived, their infection may cause them to grow even more of their parasites.
The Engineers were all set to exterminate Earth about 2000 years prior to the film, in what would have been 89-94 AD. The New Testament describes the end of the world as being imminent, to occur within the lifetime of those writing it within roughly that timeframe. The Biblical apocalypse was supposed to be the Engineers returning and killing all of humanity.
In restrospect, the trippy biblical beasties like the seven-headed leopard beast, the red dragon and the angels that look like wheels make sense as oil mutations.
You might wonder why a geologist would be involved on a mission to contact aliens. Then, remember that the crew had no idea that was their actual job on this survey ship and that the crew bets on whether the job is about terraforming. Whether the regular crew thought they'd be checking planets for hunks of valuable minerals or suitable spots for terraforming, there would still be a need for a geologist to help with either mission.
One of the Engineer-worshipping civilizations is shown to be the Egyptians, who depicted their gods with animal heads. Then you get several good looks of Engineers with organic-looking elephant-like helmets, showing how Egyptians might have got the idea.
You know, the face of the helmet strongly resembles the Typhonian beast, the unidentified animal (possibly a very stylicized donkey) whose head adorns the body of the most controversial of Egypt's gods, Set, the god of deserts and foreign lands, the only god who can actively go against the order of fate, who has been both the most hated devil and the most supreme deity in different times of the culture's history. Very fitting, don't you think? Also, all the human-faced Egyptian gods have a blue-green skin; an artistic representation of the Engineers' pallor, perhaps?
Similarly, the interior of the ziggurat, the ancient Sumerian temple, made the god's room difficult to get to and impossible to see into from the outside. A perfect way to hide that your god that's been staying there has actually died if you're a priesthood with special privileges. They also depict the gods giving humanity the waters of life (water containing life sounds familiar right from the beginning...). The Sumerian Epic of Gilgamesh also features a goddess threatening to let the dead walk the earth to kill the living. What happened to the geologist again?
The Engineers are tall, extremely pale, have big heads, and prominent black eyes. I guess we finally found out what the Gray Aliens of conspiracy theory fame were.
A subtle one: when the Engineer wakes up from his sleep pod, he does the exact same "lean over and throw up" motions that Shaw does at the start of the film.
A good deal of the Engineers' stuff is meant to resemble human tech, such as the stasis pods. Even their biosuits share the same basic silhouette as the human space suits.
Holloway's relative jerk-assy treatment of David: what if he recognized, subconsciously or not, David's obsession with Shaw, and was acting out of jealousy?
The Prometheus mission apparently cost the Weyland corporation a trillion dollars. Wasting such a vast amount of money on essentially just killing their own CEO in a roundabout way probably left them vulnerable to buyout by the Yutani corporation.
Fifield refers to his geological scanners as "pups", and one can be heard making a digitized howling noise when David finds it stopped at a door later in the film. What's a relatively common term for an avid geologist? A rock hound. Pups indeed!
The god Prometheus gave the gift of fire to help humanity. So did the ship Prometheus, in the end.
Why do the Engineers want humanity dead? Because they realise that not only are humans a dangerous experiment that has gotten out of their control, like the proto-Xenomorphs, but also when the two species are combined, the resulting creature is even worse!
Impossible, since the two "experiments" hadn't come into contact yet. Remember, this takes place decades before Alien, and the Engineers had already been planning to destroy us when they went dormant. Two thousand years ago, at least.
It's entirely possible that The Message was never intended for humanity at all! While the Engineers were observing us, we were also observing them and managed to record the information of where they were from. It's possible that the reason The Engineer tried to kill the Prometheus crew because he was having a major Oh Crap moment, realising that not only had their experiment figured out where they came from, but were now capable of getting there!
Although in general Weyland-Yutani seems to be filled with people too dumb to live, there finally is a decent reason for why they would ever want to do anything other than wipe out every Xenomorph. If word ever somehow got back of exactly what the Engineers are like and what they're capable of anyone in a position of authority would be gibbering with fear. And then they'd realize that the best weapon to use against the Engineers would be the one that the Engineers thoughtfully provided.
A frequent complaint about Prometheus is that the crew make a few stupid choices (Fifield and Millburn getting scared of the Engineer's corpse is a common one). However, consider the reveal that Peter Weyland took advantage of Shaw's discovery hoping it would be a way to extend his own life. Both Alien and Aliens showed that Weyland-Yutani were very determined when they had a goal and would go to the extremes of risking people's lives. Remember that in Alien the company said that Ash's top priority was to bring back the alien, with a note explicitly saying "Crew Expendable". In Aliens it's implied (and possibly confirmed, depending on whether you consider Alien 3 canon) that Carter Bourke had intentionally directed the colonists toward the derelict ship so they would be attacked by the aliens, then planned to infect Ripley and Newt, murder any surviving marines by sabotaging their cryo pods and jettisoning them into space just to make a profit from the specimens. All of a sudden the choices in the crew make sense- Weyland didn't have much longer to live, and saw a slim chance at the possibility of extending his own life, so he took it under the cover of being a scientific expedition. With the exception of David and possibly Vickers (who would have been the only ones in on his true intentions), he wasn't looking for the best of the best like you'd think. He just wanted a bunch of small-time people who would get him where he wanted without asking questions and who nobody would miss if something happened. Much like Alien and Aliens most of the crew was considered expendable.
The 'invitation' to visit LV 223 - depicted by the ancient drawings as the engineers pointing to a particular cluster of stars - is more likely to have been a warning to stay away. After all, there was some pretty dangerous stuff there. This mirrors the 'distress signal' in Alien, which later was found out to be a warning.
To add to that, the awoken engineer may have acted violently and decided to wipe out humanity only after realising we were too stupid to understand or heed that warning.
Why would you warn a culture where spaceflight is still millenia in their future about LV-223? Space is so vast anyway that by not saying anything Humanity would probably never find it. Calling attention to LV-223, especially to a pre-literate culture, virtually guarantees that eventually Humanity will send an expedition there.
They might not have thought that far ahead. They meant to say "if you do not behave yourselves, than something very bad will come from here", and simply didn't count on its meaning being lost in time.
Unless the message wasn't intended for humanity in the first place, but project documentation for the space-grad-student monitors of the experiment, who were supposed to stick around and god-king it up while taking notes. "If crazy-violent hyperintelligent uplifted ape project goes wrong, as it inevitably will because this movie's been made a thousand times before, refer to appendix 7-b for the location of your regional planet-wiping bio-arsenal".
If the engineers possessed the technology to make themselves immortal, they wouldn't even need stasis pods. Life support requirements over extremely long periods wouldn't be an issue because it has already been established that they can engineer practically any biological matter they need, including food.
The pods may just be there as a precaution in case they should be needed. The Engineer we see in the film, being the lone survivor, might have simply used it so he wouldn't Go Mad from the Isolation.
According to a deleted scene, the engineer angrily asks Weyland (translated through David) why you'd even want immortal life, so it seems the engineers actually do not have immortality and although create other species, are against the idea of immortality.
There is actually a striking parallell in the stories of Peter Weyland and Roy Batty from Blade Runner, both of whom are reaching the end of their lives and seeking to literally meet their maker in the hopes of receiving a longer life, only to be confronted by the inevitability of their deaths. This also becomes quite interesting when you factor in the rumours that there Ridley Scott may be planning a connection between both stories.
The Xenomorph at the end is referred to The "Deacon"Xenomorph. What is a deacon? It's a position in the Catholic church. The movie is also set at Christmas, though this isn't brought up much. Finally, the Deacon Xenomorph is born in a normally impossible pregnancy to a very religious woman. Put it all together and you have a Xenomorph born on Christmas to a woman who could not possibly have children without supernatural aid, both the woman and the child with connections to Christianity. Combine that with the mural of a crucified Xenomorph earlier in the film, and it becomes even more obvious. The Deacon is AlienJesus!