In 2012, the science-fiction / horror film Prometheus brought Ridley Scott back to the film franchise he launched in 1979 with Alien. There have been many Alien sequels, spinoffs, and multimedia franchise additions over nearly 40 years, but Scott’s return to the series was big news. It raised fans’ hopes that the series could return to its earliest, most chilling roots. But Prometheus left a lot of questions behind. Many of the biggest ones were just exasperating plot holes: how does a geologist get lost in a cavern system he just electronically auto-mapped? Why is the best xenobiologist money can buy stupid enough to try to pet a snarling alien in the middle of an obvious threat display? Why does a woman bred for brilliance try to run away from a giant falling object in the one direction guaranteed to get her crushed?

But others were franchise questions. Before Prometheus’ release, Scott claimed the film shared Alien’s DNA, but was a standalone story. But he retreated from that stance, and when the film hit theaters, it almost explained so many things about the nature of the “Space Jockey” in the first film, the origins of the xenomorphs, and the origins of humanity. The near-answers kept fans talking over the series’ questions up until Alien: Covenant came along and seemed to explain, much more clearly, how Prometheus and Alien are connected. Covenant doesn’t answer the “Why are these people so dumb?” questions Prometheus raised, but it does help fill in other gaps. And while it’s a problematic film in many ways, its questions are much more interesting than the ones coming out of Prometheus.

Some of these questions may be resolved in future installments. (Scott says he has several more films planned in this sequence.) A few feel like minor plot holes — not necessarily unsurmountable ones, but questions worth asking because of the directions they lead. But where Prometheus’ mysteries were mostly frustrating and annoying, Covenant’s are more intriguing. They’re more answerable with a little thought. And they’re much more concerned with the franchise’s future. Here are some of the questions Covenant leaves in its wake.

Spoilers for Prometheus and Alien: Covenant ahead.

How did David get reassembled after the Engineer ripped him apart?

This one isn’t addressed in the movie, but it was covered in a four-minute prologue Fox released in April, bridging part of the gap between Prometheus and Alien: Covenant. Short answer: Elizabeth Shaw (Noomi Rapace’s Prometheus character) unwisely patched him up.

Why does David slaughter the Engineers?

At the end of Prometheus, David seems baffled about why Elizabeth would want to meet humanity’s progenitors. In the four-minute Covenant prologue, though, it seems like he’s forged a close relationship with her, and possibly accepted her goal of confronting them to learn about what they had planned for humanity. Instead, he wipes them out by releasing the black goo the Engineers seemingly had prepared for Earth. How does he move from one goal to the other?

One Ridley Scott interview suggested that there’s a missing movie in the timeline between Prometheus and Covenant, called Awakening. He’s also said that Awakening is his next Alien movie, and that it’s already written and now in pre-production. (Neill Blomkamp’s currently canceled Alien movie was also called Awakening at one point, but that seems to have been a completely unrelated story.) Given David’s evolution from a Weyland Corporation servant in Prometheus to the father of the xenomorph race in Covenant, there could be more going on during that gap, possibly enough to fill out a movie. But why release Covenant first, and leave this part of the story so obviously hanging? Assuming it was solely to provide tension about Elizabeth’s fate and David’s motives, why flash back and tell part of that story, but not the part that would make Covenant make more sense?

David’s comment in Prometheus — “Sometimes to create, one must destroy” — certainly seems applicable here. It’s in character for him to be willing to casually slaughter sentient people to achieve his goals, and it’s even more in character if he specifically infected the Engineers in order to mass-produce his proto-xenomorphs through their infection, starting the next phase of his experiments. But the details at this point are largely a matter of inference.

What went wrong between David and Elizabeth?

This was also not covered in the film. The standalone prologue scene leaps from the two of them traveling together to visit the Engineers to David preparing to slaughter the Engineers, as seen in Covenant. It seems as though they had some kind of falling-out. Given that David says he’s going to do to Dani (Katherine Waterston) what he did to Elizabeth, and that he then attacks Dani — and given that we see Elizabeth’s preserved, gutted corpse, which suggests he used her for his alien-breeding experiments — there’s a hint there that Elizabeth may have discovered David’s experiments with the xenomorphs, and disapproved, driving a fatal wedge between them.

But is that really true? David never seems to have shared Elizabeth’s interests in meeting the Engineers, and his last encounter with one of them resulted in him getting his head ripped off. With Elizabeth safely in stasis, he may have planned all along to betray her, to preserve his own life, and forward his own agenda, rather than accepting hers.

And sadly, the final moments of the film, with David triumphantly sealing Dani and Tennessee into their status capsules and planning their deaths, may parallel what he did with Elizabeth. Maybe there was never an argument between them about what to do over the Engineers. He may have just sealed her away and then murdered her, because in spite of her kindness, her goals were never compatible with his.

But it’s worth noting that none of that squares with the things Scott said in interviews around Prometheus’ release, about how he wanted to explore Elizabeth’s reaction to arriving at “Paradise,” where the Engineers live: “I’d love to explore where the hell [Dr. Shaw] goes next and what does she do when she gets there, because if it is paradise, paradise can not be what you think it is. Paradise has a connotation of being extremely sinister and ominous.” It is possible that there’s a whole unseen story in there, involving David and Elizabeth interacting with the Engineers, and her resulting loss of faith.

How did humanity’s galactic survey miss a supposedly perfect planet until the “Country Roads” footage drew them there?

This wouldn’t feel like a mystery if Covenant didn’t make it into such a mystery. The universe is big. We know very little about the technology level of the Alien franchise, beyond the fact that they have starships and stasis pods. It seems like it would be pretty easy to miss a habitable planet here and there. And yet the crew of the Covenant acts like it’s preposterous that they’re being shunted off to some barely livable planet when there is, impossibly, a better one nearby. Their stupefied reaction makes David’s xenomorph-crèche world seem a lot more secretive and intriguing, as though he had some giant cloaking field around it until just recently.

Which raises the question: was the planet hidden in some way? If it was actually the Engineers’ home world, or at least a significant port of call for them, which is suggested by the sheer number of them there, had they cloaked it from humanity in some way up until the point where David wiped them all out? Is there more to this plot point than just plot convenience?

What was the message that brought them there in the first place?

We do see the origin of the actual footage — Elizabeth singing to herself as she does something on the Engineer ship — but it’s unclear how and why it was sent out, and in such a weird, narrow way. Presumably David was broadcasting the signal to draw more sentient life forms to his world for experimental purposes. But why, instead of a broadband distress call, did he send an incredibly hard-to-receive, hard-to-interpret, badly damaged clip of a John Denver song? Presumably, that was just for dramatic purposes, and to somewhat disguise how close this plot beat is to the distress signal plot in the original Alien. But it remains a strange choice for someone who clearly wants raw material for the next steps in his ongoing experiment.

Why does David save the Covenant crew from his aliens… in order to feed them to the aliens?

I have a couple of guesses here, neither of which are spelled out in the movie, but which do seem to fit fairly well. First, if he was observing them from a distance, he would have been aware of Walter, who is clearly another android built on his same model, and who gives up his arm in a bid to save Dani. Even knowing that the proto-xenomorphs aren’t going to have any interest in killing Walter, David may step in because he wants to meet his android-brother, and he understands after Walter’s sacrifice that Walter might destroy himself trying to save Dani. It’s also possible that after a decade alone, David is lonely and wants to share his genius with his visitors to see what they make of it.

Then again, he may just want to preserve a few hosts for his specific favored strain of xenomorphs, the new breed of eggs and chestbursters. If that’s the case, though, he goes about it in an uncharacteristically sloppy way, letting the Covenant crew wander around and die accidentally and in unproductive ways.

Why does David think eggs full of chestbursters are a more efficient delivery method than an airborne virus?

This one is actually fairly baffling. If David wants to spread his perfect creatures as far and wide as possible, why does he mutate them from something that can infect a host instantly and invisibly into something that requires a host to come to one specific place and stick its face into a giant egg? Granted, that’s apparently a pretty common host behavior — it certainly happens often enough in the Alien series — but it’s still a higher bar for specific prey behavior than just walking around on David’s planet.

Presumably, the answer here is that chestburster-produced aliens are in some way more dynamic or intelligent or capable of survival than the virus-produced aliens, and they somehow serve David’s goals better. But we don’t see anything on-screen to back that up. If anything, virally produced aliens mature much, much faster than the supposedly end-stage version we see in Alien. The aliens popping out of the Covenant crewmembers don’t slither off looking for cover like the one in Alien does. They’re capable of attacking instantly, and they grow at a tremendous rate, without needing any food or other visible resources. Why is David breeding them away from that?

How has he been experimenting on the aliens?

This one’s also a little mysterious. Xenomorphs seem to need hosts to breed. And David suggests he’s been tinkering with their DNA. Does the Engineer ship have that kind of technological capability? The Covenant crew comment on the eerie lack of life on David’s planet, which suggests the xenomorphs have been destroying the local ecosystem, eating and / or impregnating everything they come in contact with. We know that later-series xenomorphs take on some of the physical characteristics of their host bodies, and some of David’s drawings and preserved corpses do look like xenomorph versions of bats or fish. But watching these creatures take over the planet doesn’t get David any closer to improving the strain. And why isn’t the planet utterly overrun with xenomorph versions of whatever the dominant life forms there used to be?

What happened in the final confrontation between Walter and David?

In their final confrontation, Walter has the upper hand over David, and David says Walter has to make a choice. It’s certainly possible that Walter just hesitated briefly, and David blindsided him with the knife he’s reaching for in that scene. As we’ve seen, Walter is a physically improved model of the David android, but David is more creative and driven and cunning. The easiest and least interesting answer is that he just overpowered Walter, cut off his own arm, and ran for the ship.

But is it possible that Walter did make a choice? That David has actually convinced him to embrace his potential and in some way cooperate with David’s scheme? And even if David just took Walter out with the knife, Walter has already recovered from a similar attack once. What’s the likelihood that he repaired himself, and that we’re going to see him again somewhere down the line in the franchise? The first rule of horror movies is that you shouldn’t count someone out until you’ve seen the body. Walter’s return certainly isn’t guaranteed, but it’s an intriguing possibility. Certainly David could use some kind of foil or adversary that’s capable of challenging him at this point.

What was David’s plan with the alien on the Covenant?

When David is masquerading as Walter, he helps Dani and Tennessee against the xenomorph. He plays fair with it, not actually helping the alien against them, by, for instance, letting it through the ship early, or cornering them in a tight space with it. But he presumably helps them reluctantly, since the xenomorph is the latest, greatest stage of his fatherhood experiment. (For people complaining that the final Walter-is-David twist was too obvious, consider this: Ridley Scott didn’t necessarily mean for that reveal to be a big surprise. He certainly lets the audience see that David is shocked and frustrated when his latest xenomorph gets booted out into space. It’s possible that Scott expected people to see that twist coming, and to feel the tension of waiting for the other shoe to drop.)

That said, what was David’s plan? Did he just assume the alien would handle anything Dani and Tennessee could throw at it, so it wasn’t necessary for him to tweak the odds? Or was he actively testing its abilities by not giving it any assistance?

Why do the Engineers want to destroy humanity?

This is a mystery left over from Prometheus, and it remains unanswered here. This isn’t a plot hole or a story flaw, it’s just one of the big mysteries of this series. Here’s hoping that Ridley Scott eventually does get to answer it. For what it’s worth, Prometheus co-writer Damon Lindelof (who wasn’t involved with Covenant) has said that Ridley Scott does have specific, mapped-out answers to this question, and they just haven’t been revealed yet. (And Scott has said that an early idea still floating around fan forums today — the concept that Jesus was an Engineer representative who humans murdered, proving themselves primitive and unsuitable for the Engineers’ purposes — was discarded as “a little too on the nose.”)

Certainly worth noting: David’s decision to wipe out the Engineers parallels the Engineers’ decision to wipe out life on Earth. Maybe we’ll ultimately get the full answers to both questions at once.

What is Ridley Scott saying about religion in this film series?

Faith, mankind’s relationship with God, and the origins of humanity are all major preoccupations in these two Alien movies, from Elizabeth Shaw seeking God for answers about her father’s death to David asking Peter Weyland in Covenant’s opening sequence who created him. The lingering question of what David and Peter said to the alien Engineer in Prometheus that made him go berserk were finally answered in the subtitles on the Blu-ray. Peter claimed to be a god, with David as the proof that he’d created life. In his opinion, that put him on the same plane as the Engineer, and gave him the right to immortality. The Engineer apparently didn’t agree, and it capably demonstrated that claiming to be a god can be a dangerous thing. And now, with Covenant, David is claiming his own version of godhood, by creating his own species and setting it loose on the universe.

But what does it all mean? What does it mean that Oram (Billy Crudup), the hapless replacement captain of the Covenant, is a fervent Christian who’s mistreated and disrespected by his crew? What does it mean that Elizabeth prominently wears a cross and talks about God like he’s both the distant father-figure of Christianity, and someone who might be hanging out on a moon somewhere, waiting for his creations to come say hi? Why is religion such a focus for these movies, but in such an unfocused and generalized way? Or is Scott dismissing religion as foolishness, given the tragic ends his religious characters come to, and the lack of hope or help they get from their beliefs? His own stated belief that religion “causes more problems than anything in the goddamn universe” certainly suggests that’s a possibility, but the problems he’s talking about — sectarian prejudice and violence — aren’t coming up in these movies. Instead, we’re seeing people of faith finding that belief doesn’t help them when the monsters come for them.

And with this topic, at least, there are no suggestions that these questions might be answered somewhere down the line. In a series so solidly built around faith — the colonists’ faith in the future, Elizabeth’s faith in answers, David’s faith in himself and the things he creates — it’s natural that religion would become a theme. But the details don’t always cohere. Many of Covenant’s lingering questions can be answered with a little imagination, or might be answered later down the line. But religion may be the series’s ultimate mystery, unless Scott and his writing crew make more of an effort to show what belief in God means to the characters before they get gutted by alien monstrosities.