Why did Weyland's presence have to remain a secret on the ship? Because his company and the world think he's dead? Who cares?
OUR TAKE: That's one of those decisions where the only reason his presence is a secret is so it can be revealed to the audience. The dude is a multi-trillionaire. He built the ship. He paid for the ship. If he wants to be on the ship, who is going to say no to him? There's absolutely no reason for it to be a secret except so we can have a start-of-Act-III reveal. It serves no purpose within the plot, so we have to assume it was done for the sake of the audience only.
Is Meredith Vickers human? Is she a cyborg like David? Is she really Weyland's daughter?
OUR TAKE: Yes, no, and yes. There's a moment early on where Ridley basically underlines things and circles them in red. It's during Weyland's presentation by hologram, when he refers to David as "the closest thing to a son I'll ever have." The look on Meredith's face pretty much sums up the relationship and the insane slight she feels at having her father admit that he loves his robot more than his daughter. The reason people are having trouble with this storyline is because Charlize plays it like she's totally a robot, and there's that moment where she throws David up against a wall and holds him there while she asks him questions, even though we just saw that he's got crazy superhuman strength. There is nothing in the text that commits to the idea of her as an android, though, and while I'm sure people will tie themselves in knots "proving" it, the text doesn't support it, so neither do we.
Why do they have Vickers go through the trouble of escaping the ship at the end just to have her die two minutes later?
OUR TAKE: So they could have two extra minutes of Charlize in the film?
Honestly, it's one of the most bizarre beats in the whole movie. They do so much cross-cutting to ratchet up the tension, and she just barely makes it off, and then she almost outruns the thing aaaaand… squish. It's a strange choice, but by that point in the film, the strange choices are stacking up left and right, and her death is the least of the problems.
Why does the Engineer want to kill the humans?
OUR TAKE: That's the question the whole film hinges on, isn't it? The film goes out of its way to never give the Engineers any articulated motives, so all we can do is watch what they do and listen to the few clues that are dropped in the film's dialogue, all of which is still just speculation.
Thanks to an interview with Ridley Scott, people are now connecting the dots in a way that the film simply doesn't, and I'm not going to give the film the benefit of something the director said at a junket if he didn't actually include it in the film. There are a few lines in the film where they state that whatever happened to the Engineers happened 2000 years ago, more or less. And since the film is set on Christmas, one could assume that is not an accident. When Ridley Scott tells one person that he originally wanted to include the idea that Jesus Christ was, in fact, an Engineer and that his crucifixion was the event that caused the Engineers to turn against humanity, that is certainly a provocation. But it's not in the film. In the film, the Engineers are utterly unknowable, which then allows the filmmakers to make everything feel like it is very important while never actually committing to any sort of explanation.
What one could assume from the film itself, without any interviews or outside clues, is that at some point between the initial invitations being left on Earth and the moment where something went wrong on the planet where "Prometheus" is set, they decided that we were toxic, no longer worthy of the invitation they extended to us. They were preparing to take the black goo, which appears to be a biological accelerant, and evidently wipe us clean with it, when something went wrong, the ship was contaminated, and they were killed.
This does not address the one Engineer left sleeping, though. Based on his reaction, it seems that he is outraged at human presence on the ship, and when David tries to address him in the language of the Engineers, it sets him off on his murderous rampage. Again… without any further contextual clues, the Engineer just seems like a big dumb blue monster. In a way, this is a moment that mirrors the scene in "Blade Runner" where Roy Batty finally meets Tyrell face to face, only in that film, it is the creation that is so disappointed in the encounter that he has no choice but to kill his maker. Here, it is the angry god who reacts, throwing the last few anonymous cast members around after ripping off Fassbender's head.
The last exchange between Weyland and David as they both lay broken on the floor of the chamber sounds significant in the film...
Weyland: There's… nothing.
David: I know. Have a good journey, Mr. Weyland.
… but the entire film is full of these cryptic pseudo-heavy exchanges that sounds good without actually saying anything. I loved the open ended nature of "Lost" when it was on the air precisely because it was a TV show, and I knew they weren't going to explain things immediately. Here, though, it feels like the connections to "Alien" and the desire to kickstart a new franchise both hobble the film, forcing them to lay coy with things that should be answered while answering things that needed no answer originally.
Why does the Engineer go after Shaw? Why not just go to one of the other ships and escape?
OUR TAKE: An excellent question. First, it makes no sense at all that the Engineer finds Shaw with such speed and precision, and it makes no sense at all that David somehow knows what the Engineer is doing since he's just a head laying on a floor in a room. But the notion that he's got to kill Shaw simply doesn't track. He took off. He got in his ship and he tried to fly away, and then the Prometheus crashed into him. Why he would immediately react by going after Shaw isn't explained at all, and the later reveal by David that there are many other ships is infuriating. If that's true, are there also other Engineers asleep? If that's true, why didn't they go to Earth to finish the mission that this one ship bungled?
There appears to be a minimum of three ships on the planet in the first longshot we see. One is destroyed and crashes. That's the ship (we think) that's explored in "Alien." The second takes Shaw and David off the planet. Why wouldn't the terraformers discover the third ship in "Aliens" let alone "Alien"?
OUR TAKE: This 100% is not the planet from "Alien" or "Aliens." The film's production design seems to be confusing casual fans of the series, but eagle-eyed viewers can attest that this is a completely different planet that we've ever seen before, which means that the ships we see in this film are not the same ships from "Alien" or "Aliens" at all. Same type? Yes. Same ships? Nope.
Why do Weyland, Vickers and their staff not react at all to a bloody Shaw coming into their quarters?
OUR TAKE: This is the beginning of a whole stretch of film where no one behaves the way we'd expect people to behave faced with these circumstances. Yes, it's a big deal that they're waking up Weyland, but when a half-nude woman covered in blood with a fresh surgical incision comes stumbling into a room, you would expect people to react. Nothing. Not even the slightest hint that this might be out of the ordinary.
Why doesn't Shaw tell everyone about the seemingly frozen alien in the surgery machine so they get it off the ship?
OUR TAKE: David knows full well what happened in the surgery machine. His comment to her, "I didn't know you had it in you," in a non-too-subtle jab at Shaw, but he seems completely uninterested in following up at all, even if he's the one who started that particular ball in motion. Even when he's got Weyland to contend with, it would seem like David could find five extra minutes to walk over, check out the still-very-much-alive creature that he knows was inside Shaw, and decide what to do with it.
Again… this last act of the film depends largely on people doing things that no one would actually do. It's all in service to the plot, not in service to good character writing. The characters in this part of the movie are almost exactly as smart as the teenagers in a typical "Friday the 13th" film, and for the same precise reason.
Are Fifield and Milburn the stupidest scientists ever? Why would they go back to the one room that an alien was killed in?
OUR TAKE: As a whole, the film seems to be filled with scientists who have never heard of the scientific method. Fifield in particular is just a train wreck of a character, both in conception and execution. For some reason, he's a barking lunatic in some moments, then he's a shaky coward in the next moment, then he's smoking pot through his space suit's respirator. We see that he's the one who is running the probes that are mapping the entire structure, and that he is able to state exactly where he is because of a read-out on his suit. So why is it that he gets lost the moment he leaves the rest of the group? If he and Milburn are able to tell Janek exactly where they are when he asks, why can't they simply use the digital map they're building to find their way out? Once they are trapped inside, though, they proceed to make a series of monumentally terrible choices. Milburn, faced with a brand-new alien life form, and having already seen its terrifying little mouth, proceeds to try to pet the damn thing. This is a trained biologist? This is the guy you pick to fly to a planet where you may well encounter the first extraterrestrial life you've ever encountered? These characters are emblematic of the film's larger issues and the way things are driven forward by illogical behavior. The attack on them in the Big Giant Head room is well-staged, but it depends on them making pretty much every wrong decision that two people could make.
Is there no governmental authority on space travel? Wouldn't some body or agency need to know where this Weyland ship was going and why?
OUR TAKE: We have so little idea of the way society works at this point that it might help to see some glimpse of the bureaucracy they had to navigate to mount a trillion-dollar expedition. I am perfectly willing and able to believe that space will have been privatized to some degree by the point the film is set.
Besides, if we're going to accept that most of the crew of this trip allowed themselves to be frozen for two years, flown to a distant unexplored planet, all without having any idea why, then accepting that the ship left without telling anyone where they're going seems easy enough to accept.
If they are exploring an alien planet no one has ever been to before after an alien race has "invited" them, why is there no security crew? Why does no one have any guns or real weapons besides a flame thrower?
OUR TAKE: We definitely see some guns. They empty several clips trying to kill Fifield, to very little effect. In general, though, their behavior during the excursion is, as we observed above, totally nonsensical. When Holloway takes his helmet off because he think the atmosphere might be okay, that seems like a complete and utter breach of professional protocol. So of course, everyone immediately does the same thing, even after they see an Engineer's head explode from some sort of biological mishap. Since having a security team as part of their expedition makes perfect logical sense, of course they don't have one.
Is David evil? Why does he want to put Shaw - who never was mean to him like Holloway - into stasis with the alien in her instead of getting it out?
OUR TAKE: I don't think "evil" plays into it at all. David is simply dispassionate, utterly without empathy. When he contaminates Holloway, he's careful to first ask him for what David reads as permission first. When he realizes what's happening, David decides that studying the thing growing inside her is more important than any human compassion. Shaw is simply a subject to be studied, not a friend or a peer. It's just a matter of curiosity for him.
Of course, he's not curious enough to take two minutes to examine the thing once he learns Shaw cut it out of herself, but he's curious, nonetheless. David is fascinated by the Engineers, determined to see them close-up and at work, and he wants to see what their technology can do. He has already determined that humans hold him in a specific kind of contempt, expressed most clearly through Holloway's behavior, but in general, he feels no obligation to protect them. It's a safe bet that Asimov's laws of robotics do not apply in the world of "Prometheus."
A surgery machine just for a man? Seriously? You develop something that advanced and it only works on one sex or another?
OUR TAKE: Actually, it should work on either gender, but this particular one has been calibrated for a man. The whole reason it's onboard is to provide support for Weyland once he's awake again, so it's been calibrated for his particular biological needs. I'm guessing they could have recalibrated it for a woman, but it would have taken longer than Shaw had to do so.
When you've got two of your crew members missing and presumably trapped in an alien ship full of dead bodies, is that really a good time for the captain and the officer in charge of the mission to bump uglies?
OUR TAKE: It's like each scene in the film works fine as a scene, but when they are stacked together, the lack of logic from one to the next starts to get overwhelming. This is a good example. Idris Elba and Charlize Theron are both good in the scene and they play off each other well, but it seems like they've forgotten about any of the tensions that are building in service of a beat that goes nowhere.
Why cave paintings? And why would anybody fund a trillion dollar -- even assuming inflation -- mission on the basis of a few cave paintings? And why does Weyland assume that these cave paintings are going to lead him to people who will give him immortality?
OUR TAKE: Some big strange assumptions are made by these characters. While it is indeed odd that all these different cultures on Earth ended up painting the same pattern on walls hundreds of years apart, what's even more odd is trying to work out what actually happened. Did the Engineers spend signifiant time on Earth in the past? Did they come back repeatedly over time to make sure ancient man painted those invitations on the walls? If they really wanted us to visit them, why would their invitation lead us to a planet where they don't live? Weyland's assumption that they could extend his life essentially means that he is Roy Batty in "Blade Runner," desperate to look his maker in the eye so he can ask for more. Perhaps this is simply wishful thinking on the part of a dying man and not a logical belief, but it does seem to be a very expensive whim to indulge.
Based on the seemingly pointless presence of Patrick Wilson, do we assume that Shaw's deceased father has a greater importance of some sort?
OUR TAKE: That is a strange and distracting bit of casting considering how little he's in the film, just as it's a strange choice to have Guy Pearce buried under truly awful old-age make-up when it would have made more sense just to hire an old guy. It's not like Pearce does anything in the film that an older actor couldn't. Wilson's fine in his scene, but it does make us wonder if Shaw had more flashbacks that were cut for time, because Wilson seems to bring unnecessary star power to a two-minute role.