Prometheus give me kinds of strange feeling that much of plot in this film seems make no sense, so I have a try to find out the answers for those wired plot. All of this not just a rundown of all the questions we think still aren't answered, but explanations I searched on the net might answer it. There is not "explanation" of Prometheus, of course-- only Ridley Scott can do that, and they probably never will. I just want to give it my best shot and share my guess to you. Just for funny…
Question: Why the Engineer drinks the black goo in the beginning of the story?
The opening of the movie is stunning in its visuals, but pretty incomprehensible without any context. It’s hard to tell why exactly the Engineer-- that’s the blue muscle-bound alien creature standing by the waterfall-- has opted to drink the black goo, where is he, or really what’s going on in general, and it’s never explained in the rest of the movie, just simply left for viewer interpretation.
Guessing: The giant ship (which is different from the ring-shaped one we see later in the film, weirdly) has landed on Earth to drop off the Engineer so that he can terraform the planet and make it sustainable for life. We think he drinks the black goo to break down his own structure and spread life on Earth through his own DNA, but that doesn’t really explain his surprise while he’s disintegrating.
Question: Why does David poison Holloway?
David doesn’t have the capacity to be evil - he lacks the ability to feel emotions and simply follows directives. So why would he take the opportunity to poison Holloway with the black goo for seemingly no purpose? By the end of the film there is no explanation given as to why the android would kill one of his co-workers.
Guessing: While the rest of the crew on-board the Prometheus was looking for the origins of life on Earth and our creator, David had a very specific side mission: to find a way for Weyland to live forever. Therefore, it’s possible that David decided to dose Holloway because he wanted to experiment and see if the black goo they found would be the key for Weyland. It’s also possible he saw the black goo as the potential to create alien weapon creatures, which a company like Weyland could exploit-- though he might not have counted on that weapon attacking his crew so soon.
Question: How does Janek know that the moon is full of “weapons of mass destruction” and is just a stopover moon for them to build weapons?
Janek, the pilot of the Prometheus played by Idris Elba, largely stays out of the fray, watching from a safe distance from the comfort of his ship. But as missions members continue to disappear, Janek suits up and explores LV-223 with the surviving crew. He’s tasked with explaining what he thinks they’ve stumbled onto, explaining it as a weapons factory that’s wisely built away from wherever it is the Engineers actually live … in case things happen to go wrong with the weapons.
Guessing: This bit of descriptive dialogue is necessary to solidify the plot, and it’s best that Elba's character delivers it. But it’s more of a theory than concrete fact. From the beginning, he is written as a world-weary ship captain who has kind of “seen it all,” a cagey veteran who’s around for guidance as much as he’s around because he’s good at piloting a craft. Not that he has run into many alien weapons factories (for lack of a better term), but he’s experienced enough to know when a hostile opponent is crafting a weapon for retaliation, and we think that’s what he witnesses on the distant moon of LV-223.
Question: Why does Weyland have to hide that he’s on the ship?
From the moment the crew of the Prometheus wakes up out of hypersleep, we’re aware of just how little this group of roughnecks knows about the assignment. Shaw and Holloway are there to try to contact the Engineers, of course, and Meredith Vickers knows all about their plans, but everyone else on board seems happy to take the paycheck-- which is why we still don’t understand why Peter Weyland would have to hide that he’s on board. When he finally is revealed late in the film, it turns out he’s looking for essentially the same thing as Shaw-- so why couldn’t they have just been working together the entire time?
Guessing: Weyland seems like the kind of guy who likes to keep things close to the vest, letting his android David do his bidding and staying asleep, or doing whatever he’s doing, in his own secret chambers. We could argue all day that the movie would be more interesting if he were part of it from the beginning, but we guess the eccentric trillionaire has his reasons for keeping his distance.