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The game was in part conceived out of a personal vendetta against Irrational Games.

What little has been shown of Prey so far takes quite a few blatant cues from BioShock, most obviously the alt-history setting and the Art Déco-inspired visual style (there's even a quite familiar scene where the player walks up a set of stairs, and a trash bin comes tumbling towards them). One could also argue that it nabs the shapeshifting, tar-like aliens the from Irrational's canned XCOM shooter that was later redeveloped by 2K Marin as The Bureau XCOM Declassified, albeit that seems a bit more far-fetched.

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Now here's the thing: Prey was openly announced as another spiritual successor to System Shock (including a shout-out to Looking Glass Studios in one of the PR demo loading screens) - not a single word was hitherto wasted on BioShock, which of course in itself was supposed to be the next System Shock, but in the eyes of many failed to live up to its heritage due to being a mechanical downgrade. Prey on the other hand brings back key core mechanics, such as the grid-based inventory, and a proper, non-linear skill tree, thus making it abundantly clear what it aspires to be.

This troper has a sneaking suspicion that Arkane were at least pretty damn disappointed in Irrational's work, and in the process of creating Prey decided to stick the finger to Levine and his now-defunct team, basically saying "We can do better than you". Which of course still remains to be proven, as does this very theory.

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  • Although this theory is still unproven, what can be proven is that prey is a better, more true to system shock 2 successor.

Conversely, Prey is a part of the Bioshock Multiverse

In Bioshock Infinite, Elizabeth reveals that Columbia and Rapture are both parts of the same infinite multiverse. She states that "There's always a lighthouse, a man, and a city" and while it might be considered stretching those criteria, the space station in Prey resembles a giant lighthouse in space, is as big as a city and the player character can be a man, but also consider that the "man" part could just as easily refer to the antagonist, Andrew Ryan, Comstock... Alex Yu.

Also, Dishonored is obviously part of the same multiverse, as your base of operations is a lighthouse, Dunwall is a city and Corvo and antagonist Havelock are both men. Fitting System shock in shouldn’t be overly difficult following the same logic jumps.

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Morgan Yu is responsible for the containment breach

The other survivors will eventually try to kill Morgan to prevent The Corruption from spreading
  • The other survivors aren't really clued in to what Alex and Morgan planned, and their e-mails say as much. However, Morgan's plan, as presented by January, involves destroying the entire space station, with Morgan still on board.
    • Jossed. The only human characters to try and kill you is Walther Dahl, who is not a survivor, but rather a specialist from earth, who is sent by William Yu (your father) to secure all the research from Talos 1 and kill all the survivors to ensure there is no witness, and Alex Yu at the twist ending, when you prove yourself to be a human hating abomination and Alex's plan to give you mirror neuron to make the typhon feel empathy has failed.

The Protagonist is a clone of the original Morgan Yu.
If not a typical clone, then the first successful attempt to reprogram a Mimic. The bits that have been released all have hints that Morgan Yu themself is the experiment not the test they are running on.
  • It is. Earth has been devoured by Typhon, and Alex Yu is trying to implant memory of real Morgan Yu into a mimic to create a communication method with Typhon.

Just look at the bit where they ask Morgan to hide in a mostly empty room. A mimic's natural inclination would have been to mimic the chair, but the scientists sound intrigued if the player crouches behind the chair. If you throw the chair the scientists begin getting worried about glass breaking. Given how cutting edge the lab is suppose to be, why would the scientists be worry about a ordinary human being able to break glass designed to keep the subject and the observers separated?

  • The player/Morgan will get an optional neuromod upgrade that lets for shapeshifting. Yes, Morgan can at least become a mimic if not born one.

Speaking of separated, why simulate a sprawling city for Morgan, including a faked helicopter ride? An email mentions a violent outburst from the subject of some experiment. The subject is not named but its memory of the event is gone by the next set of tests. Why have the alarm clock in Morgan's apartment read the same day every time they wake up? sounds like they're stuck with anterograde amnesia and someone is taking care not to disturb them with that knowledge.

All of the above could be coincidences and red herrings.
Maybe Morgan just has some form of anterograde amnesia and the tests are their brother trying to cure them. Maybe the aliens have nothing to do with Morgan Yu at all.

  • Jossed, jossed, jossed. Our Morgan was born a Mimic, and Alex's ultimate scheme was trying to see if Typhon could be taught to live in peace with humans.

This is all the Tau's fault
Some of the Ethereals somehow managed to hitch back a ride in time to humanity's distant history, and knowing some catastrophe was going to drive the beginnings of the Dark Age of Technology, decided to create that catastrophe by introducing humanity to the Typhon-a member of their Empire in the present era, having learned to feed on the life force of nonsentients. It was their belief that, if humanity discovered the Typhon could be made friendly, the Imperium would become much less of an Absolute Xenophobe. If you've been a bastard, they've done nothing except close a Stable Time Loop, as Mimic Morgan seems just as cruel and ruthless as a human as they do as a Typhon, but if you've been an okay person, they've pulled off something brilliant.

Humanity will eventually colonize a new world in a different dimension
And that world will become the future setting of Dishonored

Alex is planning to merge humans and Typhon into one species
The existence of Typhon-based neuromods indicates that humans can acquire the same powers (energy manipulation, telepathy, shapeshifting) the Typhon have. Alex's own experiments indicate that human-based neuromods can be implanted into Typhon organisms to give them human qualities they lack (i.e. empathy). But what would happen, if enough humans were implanted with Typhon-based neuromods, and enough Typhon were implanted with human-based neuromods? They would have the same physical and metaphysical capabilities, and they would think in the same way. Any difference between one species and the other would be erased.

The final scene is still a simulation
In the final scene, you learn the truth about yourself - you're a Typhon that's been reliving Morgan's memories, in an attempt to make you bridge the gap between humans and Typhon. Unless you were incredibly vicious during the main game, you then have a final choice to embrace or reject humanity, killing Alex if you reject it. Given a lot of the actions you can take and still be given the choice, it seems extremely foolhardy of Alex to offer this to you so readily, especially since it's implied that you're not the first Typhon he's tried this with. So instead, Alex sets up a second simulation that is very similar to the real world, gives his judgement on your actions, and allows you to choose to attack him or embrace humanity in one final test. If you attack him, then he puts you down in the real world and tries again with the next Typhon. If you embrace humanity, then you've proven that you're (reasonably) trustworthy when presented with the truth of the world and not just a simulation where you believe you're human, and he wakes you up for real sometime shortly afterwords.

The game is a prequel to System Shock
The game really hammers home how advanced the AI in the Operators can be, and makes a big plot point of uploading the voice samples of one Archival Chief Danielle Sho to one such Operator. At the end, Danielle has had her whole consciousness replicated in an Operator. Meanwhile, assuming the Earth survives, Transtar is left in a tight spot. Let's say another megacorp, like Trioptimum, buys up the remaining Transtar tech including their space stations and Operators. They change Dan Sho's name to SHODAN to conceal her origin, and claim her as their own invention. 37 or fewer years after the invasion, she ends up operating the Citadel Station research satellite, just as an archival AI would, and the rest is history. Want proof? The game was tentatively named Danielle during its production as evidenced by the PC version's EXE file being housed in a folder with that name. It was her origin story all along.

Mooncrash's canonical events
If we can assume that all story quests are accurate, then there appears to be a conflict between the story quests for Andrius and Vijay, and the gameplay. Namely, there is one escape pod, yet Andrius is seen using it to transport the mimicked doll, and Vijay sees Claire escaping in it. Or does he? She responds as if he's foiled her plan if you crash it, but this could be just another layer of subterfuge used by an extremely tricky saboteur to cover her tracks. It's entirely possible she was simply watching the escape pod from somewhere else, waiting for her chance to leave undetected. If that's so, then her plan unintentionally prevented the mimic Andrius left in it from reaching Earth.

A Possible Timeline and the fates of main characters.
Due to the way the story is told, it isn't always clear which events take place in what order, especially considering we don't get to see every important event at all. Here's my suggestion for the order of the story objectives:
  • The first story in the timeline has to be Riley Yu's, where she test-fires the kill towers. This clearly takes place well before the outbreak, by days or possibly even years.
  • Next is most likely to be the beginning of Joan's story, where she kills a scientist. Since he's in his office as normal, this would appear to take place just before or just after the outbreak. I would speculate that it takes place just after the alarm is raised. The threat finally pushes Joan to drastic action to locate Brian Chung, because if she doesn't try and find him before they evacuate, it's likely she won't ever meet him again. Ironically, this probably saves her life if the vast amount of dead bodies by the shuttle is any indication. There's no way to tell how long her story takes, but she would have to break into highly secure areas, so definitely after the security have abandon pytheas labs.
  • After that, Claire's, because her story has to take place right before Vijay's. Since the security team is after her rather than fighting the typhon, this has to take place pretty much right about when the typhon break loose, any later and all security personnel would be redirected to fight the typhon. She's probably in a similar situation to Joan, not expecting the typhon but taking advantage of the chaos to pursue her own goals.
  • Which is followed immediately by Vijay's story. There's even room for overlap with Claire's story depending on how long it takes him to shake off his hangover and get down to the moonworks. This is also our first confirmed character death. Claire is down.
  • The next event is Andrius' story. Starting his story skips the corruption level to 4, regardless of what it was on before. Presumably this is to indicate that there is canonically much higher numbers of typhon in the station at this point after having fed on all the crew. So this takes place well into the outbreak. At the end of his story, Andrius dies.
  • Additionally, Vijay dies some time after killing Claire, but before the next point in the timeline. We know this because his dead body can be found and tracked from a security station. Since the simulation is built from records on the data vault operator, then the station must have had records of Vijay's death before the vault operator as ejected into space.
  • The very last event we see must be Riley's "escape", where she backs up all the base records and herself. We know this has to be the last event we witness because of the nature of the game as a simulation. Since everything we see is part of a simulation created by the records that Riley saves in this sequence, which she then shoots into space, then any event that happens after this can't be a part of the simulation, because the sim has no records of it. Due to sabotage, Riley dies in the act of doing this. Sort of.
  • So in summary, Claire dies first. We don't know how long Vijay lasts after killing Claire, but if he dies to Claire's toxin, then not long. But it could be that he holds out for a while, possibly outliving Andrius but due to the fact that the data vult operator has records of him being dead, then he must die before Riley. Which leaves only Joan. She's the only one who isn't confirmed dead. Curiously, she can't be tracked through a security station, but neither does it say that she's dead. Which leaves two possibilities: firstly, that she's still alive and hiding on pytheas when Riley uploads herself, or secondly, that she actually escaped and is out of the tracking bracelet's range. Both are possible. With a fabricator and some turrets, she could hold out for quite some time if she chose the right spot to defend, until a technopath comes along at least. But it's not likely that she escaped. Mainly because only one escape route would work for her. Escape pods are out, Andrius and Claire saw to that. The mimic portal requires Claire and Joan to cooperate, which is highly unlikely. Only Riley can upload herself. And she can't have escaped in the shuttle because it's still there when Peter crashes near Pytheas at the end of the game. Which leaves only the mass driver. It's more likely that she dies on Pytheas just like everybody else, but she is the one who holds out longest. But there is a slim chance, which would make her Pytheas' one and only survivor.
    • One point of contention: there's no reason to assume the shuttle taking Peter to Earth is the one from Pytheas. Indeed, I rather doubt it, as KASMA putting his satellite right near Pytheas is just asking to get it noticed. Peter seems to have been shuttled home from the Moon colony.

The Fate of Talos 1.
Following the reveal at the end of Prey, everybody assumed that Talos 1 wasn't really destroyed or saved, and nobody escaped on the shuttle, due to the implication that Morgan Yu is in fact dead, and the Earth has been taken over by the Typhon. At the time, it was the only thing that made sense. That these "win" scenarios were fabricated just for the simulation. However, Mooncrash shows us how the Typhon got to earth, twice over, both times from Pytheas, not Talos. Which means that while the fate of Talos 1 is still unknown, it opens up the possibility that Morgan Yu really did destroy the Typhon on Talos. Possibilities include:

  • They followed the nuke ending, destroying Talos. Either a small number of survivors escaped on the shuttle, or Alex alone escaped in his own pod. Morgan either goes down with Talos or later perishes on Earth.

  • They deployed the nullwave, saving Talos. If they are dead in this scenario, they must have died on Earth.

The Operators at the end were not uploaded brains.

At the end the impression is given that the Operators with Alex are the uploaded minds of the characters speaking. But of the four characters only Igwe seems likely to want to upload himself, with the other three being opposed to the Typhon based tech in various ways. While it's possible they had a change of heart I think it's more likely that they are still alive and human and remote operating the Operators. This because putting all of them plus Alex into a room with a creature that may choose to kill them all would be deeply stupid. Alex being there may be considered an acceptable risk to establish trust but all of them would be an absurd risk.

The actual leader of the Typhon.

The Typhon never seem to have seriously threatened a containment breach before, even though they've had plenty of opportunity - the original station was built around completely-uncontained Typhon, yet they don't seem to have caused any problems for it at all. Why did they suddenly become a threat? Well, they would need to have someone directing them. A mind capable of actually understanding their situation rather than just reacting to it reflexively the way lesser Typhon seem to. A mind that understands humanity well enough to subvert the available defenses, and with enough influence over the station to get the Typhon to earth despite the numerous security procedures. A mind like the real Morgan Yu, who repeatedly exposed themselves to Typhon neuromods and was clearly fascinated with the Typhon to begin with. In the real-world timeline, Morgan went through a plot arc that mirrors the players', but in the opposite direction. Possibly in reality the reason they were wiped and imprisoned was because Alex Yu realized they were a threat; but they were eventually able to - consciously or subconsciously - direct the Typhon and escape. What happened to real!Morgan is deliberately vague in the game, because nobody wants to tell you that they are leading the Typhon. Likewise, when you hear that voice in the moments where the simulation nearly fails, telling you to side with the Typhon, it sounds like Morgan. When first playing through you might think it's your own internal voice - but why would a Typhon have Morgan's voice representing their inner self? No, it's the real Morgan talking to you through the link they use to command the Typhon. This also explains why Alex wanted to turn a Typhon into Morgan specifically - they need someone who understands how Morgan thinks and who can potentially contest Morgan's control over the Typhon.

The Recycler Charge was developed to remove corpses
Neuromod production creates a lot of bodies, rather than incinerate then some body came up with the idea to feed them into a Material Recycler, but that required cutting them up first. However a single Recycler Charge can dispose of several bodies, with the material created from this being useful to make tools and other things. Considering all the other inhuman things the Neuromod staff did this doesn't seem unlikely.

The Typhon have very poor hearing
Notice how so many Typhon make noise that gives them away? It's because they can't hear them selves making that noise and think they are being quiet.
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