Prey is a game about choices. It will most likely be discussed among friends in relation to whether or not they killed the prisoner in Psychotronics. Because of these choices and others, the game can end in several different ways. Did you make the right choice?
While there are many smaller variations in each ending (particularly in regards to the game's epilogue), the game ends in three main ways. Let's talk about these endings.
[Spoiler Alert: Below are story spoilers.]
Abandon Ship - Leave Early Via The Escape Pod
This is perhaps the earliest way to end the game. You do this by completing the "Who is December?" mission, which grants you the achievement Abandon Ship.
As you recall, early in Prey, you are contacted by an Operator named December, who insists that January is up to no good and that the real Morgan Yu created December as a fail-safe in case things went wrong. December informs you of an escape pod above Alex Yu's office, and sends you on a complex path to getting it.
After January kills December, search her corpse to reveal the key code to Alex's safe. In Alex's office in the arboretum, there is a crate blocking a maintenance hatch behind his desk. Move the create (requires Leverage I) and open the hatch to access Alex's safe. Open the safe to get a keycard to Alex's Cabin in Crew Quarters.
Note that at one point during the "Who Is December?" side mission will have you search for the keycard in the Simulation Debriefing room of the Neuromod Division. There is no need to do this, as it is a red herring. Simply go to Alex's safe and then to his cabin.
When you get to Alex's Suite in Crew Quarters, the EP101 keycard to unlock his escape pod is under a potted flower on Alex's nightstand.
After getting his keycard, head back his office in the Arboretum. You will either need to hack into his computer to extend the rooftop bridge (it requires Hacking IV) or use your GLOO Cannon to climb to the railings above and carefully walk over. Once to the escape pod, use your EP101 keycard to open it. Get inside, hit the close button behind you, then click "initialize launch" on the computer screen inside and then press OK.
Ending explanation: Ending the game this way will play a brief audio file from Alex lamenting how you are "giving up," and then go into a strange ending screen where you hear a voice saying "this isn't the one. Start over." Credits do not roll at this point. The game will merely ask you to reload your last save or return to the main menu.
A Mind Without Limits - Kill All the Typhon
The entire ending choice boils down to whether or not you choose to go along with January. The "Mind Without Limits" option is the one that doesn't go along with January. As you go throughout the main story objectives, you will eventually be given a Prototype Nullwave Fabrication Plan. Fabricate the prototype Nullwave device and then bring it to Psychotronics.
Once in Psychotronics, go toward the access tunnel to G.U.T.S, but instead go the the containment center and place the device on the Heart of the Coral. You then have to go to the Command Deck to activate the Nullwave device. There, you will find January confronting Alex (assuming he is still alive in your playthrough). If you do nothing, January will incapacitate Alex and will not allow you to activate the Nullwave device unless you kill her. Whack her once with a wrench, search her corpse for loot, and then activate the Nullwave Device.
Ending explanation: Once you activate the device, a cutscene plays showing that the Nullwave Device was successful and that every Typhon aboard Talos I died, including the Alpha Typhon that attacked in the last act.
Perdition - Destory Talos I
If you opt to side with January, you'll need to go through a lengthy series of events in the Talos I Power Plant and Reactor to get both yours and Alex's Arming Keys. Once you have them, put the arming keys in the Reactor Room, and go to the Captain's Loft in the Talos I Bridge (accessible via the Arboretum).
Inside the Captain's Loft, you will see a similar scenario to A Mind Without Limits - Alex and January arguing over whether or not to destroy Talos I. If you still want to destroy Talos I at this point. Again, unless you intervene, January will incapacitate Alex. If you choose to intervene, but still opt to destroy the ship, Alex will choose to go down with it, so there's not point in intervening just yet.
January will not let you escape the ship after initiating the destruction sequence. So, if you want to attempt an escape, you'll need to kill January (before initiating the sequence, just to be safe). You can, however, also opt to go down with the ship.
If you decide to kill January, but still blow up the ship, you have two options for escape. If you want to escape with the others, you'll have to go to the Shuttle Bay and escape with Dahl (assuming you incapacitated Dahl and worked with Dr. Igwe to trick him into launching an escape mission). If you saved Dr Igwe, Sarah Elazar, Mikhaila Ilyushin and the prisoner, Aaron Ingram, they will all be aboard. Anyone you didn't save will not be aboard the ship.
If you didn't save Dahl, but still want to escape, you will have to do so via Alex's escape pod. Assuming you've taken all the necessary steps, you can still access his escape pod via the Arboretum. This will play a different sequence than the Abandon Ship method of ending the game, since your mission is now complete.
Ending explanation: After either launching the escape pod or taking the seat next to Dahl, a cutscene will play showing your ship barely making it beyond the explosion, which evaporates all the Typhon and Talos I itself, before rolling the credits.
Epilogue - After the Credits
If you seem unsatisfied by the pre-credits ending, no matter which one you choose, you aren't alone. Was my choice the right choice? Was December actually corrupted, or was January trying to mislead me? Did any Typhon make it back to Earth? Could I have stopped them? The pre-credits ending doesn't answer any of those questions.
Then the post-credits scene plays. It's always the same, no matter what ending you chose or other choices you made throughout the game. And, while opening up an entirely new can of worms, it also doesn't answer many of those questions. In fact, it makes you wonder if even asking those questions was relevant at all.
You'll be in front of Alex YU and four Operators that now house the consciousness of Dr Igwe, Sarah Elazar, Mikhaila Ilyushin and Danielle Sho. They will then recap the various choices you made throughout the game - whether or not you saved Dr Igwe, helped out people in the cargo bay, got Mikhaila's medicine or helped out Danielle.
If you made more empathetic choices, they will opt to let you live, and you can choose to either help Alex or kill all four of them.
As I alluded to in my review, this ending, which is the same no matter what happens, undermines all the choices you made throughout the game. There's not necessarily a "good ending" or a "bad ending," as no choice you can make will change the end result. This will always have been a simulation, and Earth will always end up overrun with Typhon.
Perhaps the real Morgan made the wrong choice, which led to that fate for Earth, and the simulation obviously couldn't change that, but Prey couldn't be bothered to explain that one way or the other. At one point, you find a USB drive with damning evidence of inhumane practices aboard Talos I. If you escape, surely you'll expose this? Did whether or not you blew up a ship approaching Earth that probably had Typhon aboard have anythign to do with Earth's fate? Well, having finished the game, who knows?