Why does Michael Fassbender's android slip some gooey alien poison to Logan Marshall-Green?
The motives of David, the silky robot played by Fassbender, remain inscrutable throughout the film. Yes, Marshall-Green's character has been a dick to him for most of the movie, but what does David plan to accomplish by mutating him through the goo? Could he possibly have foreseen the wild chain of events that would lead to Marshall-Green then impregnating Noomi Rapace with an alien baby who spawns another, more familiar Alien with an Engineer? Or was David just feeling peeved that day? Either way, the android was putting the entire mission -- and crew -- in jeopardy.

Why, then, does he save Noomi Rapace at the end of the film?
Pulled apart but still sentient (a la Lance Henriksen's Bishop in the previous Alien films), Fassbender's David gets back in touch with Rapace at the end of the movie, gives her help and advice, and then they team up together. Why? Why is he helping her now after he did her dirty by essentially killing off her boyfriend? Boy, is that conversation gonna be awkward in the sequel.

Does the first scene take place on Earth?
In the striking first sequence, an Engineer on a far-off planet essentially donates his body to science, swigging a potion that causes him to dissolve into tiny DNA bits that will most likely create new life. Is that how life on Earth began? Probably ... and yet in interviews, Ridley Scott says the planet might not even be Earth. It's a sidestep akin to the one in the movie's final sequence: You do get a crashed ship, an alien, and a chest-burst Space Jockey ... but they can't be the ones seen at the beginning of Alien, because the Jockey's not in the right ship. The movie takes you right up to the edge of an answer to its own question, then feints to the left.

Why is everyone such a jerk?
We suppose that speed-of-light intergalactic travel followed by extended vomiting would make anyone a little fussy, but still: Everyone on this crew is an asshole! Charlize Theron doesn't really get to develop her character past "bitch," Michael Fassbender's robot conceals those mysterious-but-malevolent motives, Logan Marshall-Green insults robots and swaggers around like he's trying to pick up the most numbers at a frat party, and Guy Pearce screams to Noomi to shut up -- and has her hit -- in front of the alien Engineer they're trying to woo. In fairness, Noomi was pretty petulant in that scene. It's a wonder they didn't all kill each other before takeoff.

Why doesn't anyone care about Noomi's self-Cesarean?
Noomi escapes her restraints and attacks fellow crew members in a desperate race to the medi-pod, where she removes an alien from her stomach in a bravura sequence ... and then everyone pretends like nothing just happened? Those staples are huge! Shouldn't another crew member at least ask where she got them, and whether it involved the horrific mutant alien fetus they all knew about a few scenes before? Also, was there no random junior staffer she could recruit to go check on that critter? Seems pretty easy: "Hey, Junior Lieutenant Chuck, could you run back into the surgery room and make sure the giant squid baby I just ripped from my stomach isn't still alive and growing at an alarming rate?"

Why doesn't Idris Elba care what's going on with his crew?
Doesn't Idris seem weirdly disinterested in all the super-dangerous mapping and crew members going lost in that alien pyramid? He's the guy who's got a whole 3-D map in front of him, and yet instead of guiding his scientists from room to room, he wanders off to screw Charlize and appears pretty nonchalant when people die because he's not really paying attention to them.

Is Charlize Theron basically cosplaying as Samus Aran from Metroid?
Well, you tell us. (The answer is yes.)

Why do the two scaredy-cat geologists suddenly seem so taken with the "cute" little alien?
Those guys are wusses who beg off the main mission because they don't want to disturb any aliens, but moments later, they're ready to cuddle up with the first clearly threatening little alien monster they see. They should have known better: We're positive that "Don't Touch the Baby Worm Aliens" is a class you have to take in Space Geologist School.

Why cast Guy Pearce as Weyland, and not an actual old man?
Since it's Pearce under all that old-age makeup, you assume that the elderly Weyland will eventually find that fountain of youth he hope the Engineers can essentially lead him to. Nope! Weyland is killed off right after he finally shows up in the flesh. So, why bother casting Pearce instead of an actor who's actually the same age as the character? You might assume that it's so Pearce could film his TED talk tie-in, but this open question kind of has an answer: Scott and Lindelof actually cut a scene from the shooting script where Fassbender's android would interface with a young Weyland by tapping into Weyland's dreams. Still ...

Why couldn't Patrick Wilson catch a break?
Only one quick flashback scene, and ebola? It's not his year.