Warning: Many, many spoilers below.
Beyond terror, the Alien franchise has always excelled at generating one thing in particular: unanswered questions. Where did the aliens come from? Why would anybody even try to control these things? Why couldn't Ripley ever just get a break? And, wait, what did that ending mean exactly? The latest film, Alien: Covenant, continues the tradition. Even though it answers some of the biggest questions fans had at the end of the last entry, 2012's Prometheus, it raises plenty more. Including:
Did the Weyland company sponsor the Covenant's mission?
Why was Walter (Michael Fassbender) onboard the colonist ship Covenant? Is this a Weyland-sponsored mission or has Walter become the iMac of droids in this timeline?
Why didn't the mission spot that planet perfectly capable of sustaining human life (and Earth wheat!) before venturing forth?
A random, cataclysmic event that halts a space ship right next to the planet David (also Michael Fassbender) is living on is believable enough. As is the fact that that event happens to kill the ship's captain who might have actually listened to his wife when she said, "Umm, maybe we shouldn't go poking around a strangely perfect planet?" But the crew makes a point of having missed this Earth-like planet precisely when they were looking for an Earth-like planet to colonize? How? Maybe the alien civilization that lived there before had cloaked it somehow. But this series of unfortunate coincidences is never really explained.
Why didn't they strap those sleeping chambers containing the colonists down more tightly?
The Covenant's cryo-chambers were swinging around wildly like candy in an old vending machine anytime the ship hit turbulence. Click it or ticket, space explorers.
Why is James Franco in this movie for about two seconds?
Franco plays the rightful captain of the Covenant. He also dies horribly within the first several minutes of the film. His only real lines are delivered in a video message that looks like leftover 127 Hours footage. According to Google, he was in this prologue scene that's not actually in the film. But still, he's mighty expensive for a cut-out cameo.
Who would put James Franco and Danny McBride in charge of a colonization mission?
Have the people at Weyland never seen Pineapple Express?
Why didn't the crew wear their helmets on the planet?
This has to be in the space colonist manual for exploring planets: Never, ever take off your helmet on a new planet—at least not until the biologist on board has taken some soil and air samples. Who knows what kind of pathogen could be floating around? You know what kind? The kind that turns you into an exploding alien incubator.
What's the deal with all that wheat?
The crew finds wheat on the planet. It's astonishing! (And pretty.) But who planted it and why? Was it David? He's an android that doesn't eat food. Was it the Engineers before they all got murdered by David? If so, why? Is this distant planet wheat that was brought to Earth or Earth wheat that was brought to this distant planet? Botanists need answers too.
When they figure out that they may have found remnants from the Prometheus expedition, why don't they leave immediately?
This is a classic horror movie question. If you find Dr. Shaw's (Noomi Rapace) dog tags, that's a decent sign of something wicked this way coming.
How did Shaw put David's head back on?
David was decapitated toward the end of Prometheus. So, having boarded an alien craft, how did Shaw put android Humpty Dumpty back together again? Did she have super useful welding/robot building tools on that ship they escaped on? Why wouldn't those same tools be on the Covenant to fix David's arm when it gets cut off later?
Why did David kill all the Engineers?
David has expressed his disdain for the human race. But he doesn't know much about the engineers. In fact, they're supposed to be gods, much more advanced than humans. So if he's in search of the perfect race, why kill them all off? His objective may have been creating thousands of newly bred aliens by pouring the black goo on them, but it seems to either have just killed them or made all the aliens kill each other off. Even for somebody who loves Lawrence of Arabia so much, killing all life on the face of the planet soon as you show up seems extreme. He could have just experimented on a few first.
How did David crash land?
We see him pouring goo on the Engineers from a spaceship floating above their city. But earlier, the Covenant crew finds the same ship crash landed far away.
When did David kill Shaw?
Prometheus seemed to be setting up Shaw to become the new Ripley, so it's a surprise to find Shaw has died in Covenant. If we can assume that David killed Shaw because he loved her (as he says) and thought she would make a good alien hybrid, did he do it before or after he killed off all the engineers?
Why would Oram (Billy Crudup) stick his face in a mysterious egg-flower with a moving embryo in it?
Especially when an obviously creepy droid that just yelled at you for killing his alien friend says that the embryo "has been waiting" for something. That something is you. Run.
What was with that kiss?
Did two people on the CGI team make a bet about whether they could make Michael Fassbender kiss himself in the movie? There will presumably be a lot of Michael Fassbender fanfic authors who will be deeply disappointed by the awkwardness of that scene.
And what was with that other kiss?
David locked lips with himself or, worse, his "brother." So now he wants to kiss Daniels (Katherine Waterston) too? What is the purpose of this? Is this a power thing, like a sexual assault? Does he see Shaw in her, whom he admitted he loves? The "Is this how you do it?" line did not help.
Why didn't anyone ask the android they thought was Walter any personal questions, just in case it was actually David?
Maybe the crew of the Covenant hasn't watched many scary space movies, but when someone's twin or clone or doppelganger comes running out of nowhere to join you on your mission, you pause and quiz them on personal background information to ensure that this is the good droid, not the bad one. This is also probably in the manual.
Speaking of which, how did David kill Walter, cut off his own arm, change into Walter's clothes, swallow a couple alien embryos and still outrun the Alien out of the cave?
Seems rushed for someone as obviously fastidious as David.
Why couldn't Mother turn down the music in the bathroom when the alien was attacking the couple in the shower?
For an all-knowing spaceship program, Mother is pretty useless. She can't alert the crew immediately when a foreign biological agent is on board. She can't detect the difference between David and Walter's presences or voices. And even when she does know that there's an alien in the bathroom, she can't turn down the sexy music to warn the couple therein that they're about to die a very naked death.
What's David's deal?
So David wants to create a species that's superior to humans. Fine. But are the aliens he's creating really that? David's reciting poetry, and the creatures he's creating are just killing machines. No higher culture. No ability to not eat each other apparently. Is being a god worth it if what you create is pretty basic?
What's up with David getting Byron and Shelley mixed up?
There's a seemingly meaningful moment when Walter catches David in an attributional mistake. It would be a profoundly embarrassing faux pas at an android cocktail party for sure. But we're never clued into what that meaning is exactly.
Why did the Engineers want to destroy humanity?
A lingering question from Prometheus: The Engineers were planning on destroying their "failed experiment, humanity, but we never learn why. David Lindelof, who helped write Prometheus, said there was "one answer" in the films. Good luck finding such a thing in Covenant.