Man....when you really look into it, SOMA is such a hard-hitting game. The feelings you get when playing are so genuine and perfect. I'm going to sum them up here, in spoiler boxes, so you don't see something you had no control of avoiding if you don't want to accidentally spoil yourself.
When you first wake up in Upsilon, at first, you don't understand a lick of what's going on. All you know is you have an omnitool, you're no longer in Toronto, Canada, and 88 years have passed. Technology has majorly improved and advanced, and everything somehow still seems generally understandable, even if you're 88 years behind in the knowledge of technology. Finding out that a comet known as Telos killed pretty much everything on the Earth's surface (on January 12th, year 2103) had to have hit as hard as the comet did. You realize that you're the only actual, normal, surviving being. You're not even human anymore at a later point. Though...you're still the only one properly alive (not counting the monsters).
Under the Sea:
The fact that you can explore parts of the ocean, and see all the docile and hostile wildlife and creatures is incredible. You're even able to explore a sunken ship. It shows that Pathos-II was doing a lot more research than you could possibly imagine, and that they must've gotten pretty far before the comet wiped out everything on Earth. You begin to realize just how lucky you and Pathos-II were to survive. Still, being able to explore the ocean must be pretty unsettling, considering you're technically the last surviving human.
What Makes You Human:
Continuing from the 'last surviving human' point made, let me explain. It shows that you're somewhat human, near the end of the game, when your arm's torn off by killing the rogue program known as the WArden Unit (WAU for short), the thing responsible for all the monsters you face in the game, by jamming your structure-gel filled arm into its heart (structure gel keeps you alive, but it's like poison to the WAU), and seeing your arm bloodily ripped off. You survive, though. You also had the option to let it live, apparently. Still, the fact you're apparently the last surviving human (well, human-robot; not a cyborg, either), is just bizarre and unsettling.
Hints and Clues:
The notes, entries, and audio recordings you find throughout the game really do show just how in-depth the game's story and situation was. People going rogue, backstabbing, betraying, suffering and experiencing unusual illnesses - the likes of one that literally causes your head to explode - really makes you wonder what truly happened here. What really happened in the case of the aftermath of the impact? I'll note those in another spoiler box, but the mysteries that are easily solved, or solved with minor or major convolution and difficulty really does give depth to the game's overall storyline.
A Friend and Her Plan:
You're not alone the entire game, thankfully. You eventually make contact with and find someone else, named Catherine Chun. She's not exactly a human, but she IS conscious and somewhat alive. You and Catherine slowly begin forming a close friendship over the course of the game, and work together to make your way to the game's MacGuffin, the ARK. The ARK is essentially a computer world that was made to closely resemble or perfectly imitate Earth, back when it was glorious, healthy, and beautiful. People would have their brains scanned and uploaded onto the ARK, in an attempt to save mankind. It would be loaded onto the Omega Space Gun, a large underwater gun built to launch spacecrafts into...well, space, obviously. Unfortunately, Catherine ran into some slight complications, such as John Strohmeier threatening to shut down the ARK project in the past, because people believed that by killing themselves, they would wind up on the ARK. (Hey, people, here's a suggestion - How 'bout living life to the fullest, and THEN when you die, you'll wake up on the ARK? Then you'll have two long lifetimes to live!)
It's revealed that Catherine took a wrench to the head in a scuffle, while trying to convince two other scientists in the room, who were unsure if the ARK would survive the launch into space, to launch the ARK You find her body in the room where the ARK's space probe was located (not the ARK itself, but the bullet-like probe that would launch into space).
The Warden Unit (WAU), as mentioned before, is an AGI (artificial general intelligence, as the Soma Wiki calls it), that was made by Carthage Industries, and was meant for performing maintenance tasks all over Pathos-II, which I forgot to mention, is the name of the underwater station you're in. A man named Dr. Johan Ross was its main overseer and operator, again, as the Wiki says. It eventually went rogue, and caused these unusual black, tentacled things called growths to grow and expand on, in, and around most of the machinery and structures throughout Pathos-II, causing robots to malfunction and go insane (the first one you meet being the Construct.)
The WAU's reaches can be distinguished by its iconic blue glowing spots. And yes, it's even gotten to humans, too. You actually do find a few non-insane robots and human survivors who were supposed to die, but the WAU wouldn't let them, therefore injecting them with its growths, helping them live...unfortunately, that brings me to the two final points that hit me hard.
A Tough Choice:
Throughout SOMA, you will encounter said human and robotic survivors. You'd usually find them connected to some kind of power source. The painful thing about these situations is not just the fact that they're completely helpless, but also that you have no choice but to unplug the cords that are keeping them alive, like shutting off a life-support machine. You don't have a choice, because the power sources they're connected to are usually the power sources connected to things like doors, vent locks, lights, and terminals...and you need that power to continue in the game. It hurts to watch as you painfully unplug the cords, and watch what could've been a survivor slowly die. One tragic example is Robin Bass, a robot that you find near the entrance to Theta, one of Pathos-II's facilities (others being Upsilon, Omicron, Lambda, Phi, and Tau.) The sad part here is that throughout the game, the robots you find don't realize that they're not actually human. These specialized robots are the result of people who have died being moved onto the ARK. Their robotic forms are formatted with their human consciousness. As Simon puts it, 'Someone would just shove a picture of my brain into a suit and hit the power button'.
These robots truly believe they're human, and Simon almost decides not to conceal the illusion of her current state. You're then given the option to unplug her power cord, because you wouldn't want her living like that...it's a truly painful situation, and I can only imagine that what it does is effectively kill her in the ARK. I wouldn't know for sure, though. And right near the beginning of the game, you find a man named Carl Semken...well, it's actually his dead body. You then find his robotic consciousness in an assembly line, taking up power that you, again, must use. This results in you having to pull a switch that rerouted the power, and painfully shocks Carl. It doesn't kill him, but being forced to listen to his pleas and screams to end the torture is so unbearably sad, that I literally shut the switch back off, then realized I had to turn it back ON to continue....I feel horrible about it still.
The Punch In the Gut (ENDING SPOILERS):
Oof, this one's gonna hit hard. At the end of the game, you and Catherine successfully make it to the Omega Space Gun, ready to launch the ARK. In short, you successfully get yourselves scanned and uploaded onto the ARK, and it's shot out into the infinite, lonely reaches of space. And then...here's where it hits like a truck: The realization. Earlier in the game, Simon Jarrett (the game's protagonist) asks Catherine if the two could somehow get onto the ARK, to which she basically tells him yes. But that's when the painful realization hits both you and Simon - she didn't realize he meant actually transferring himself ONTO the ARK. Let me explain this in simple terms.
When you're uploaded onto the ARK, you're not moved onto it, unless you possibly die, if that even works. Think about when you copy a file on your hard drive, thumb drive, external hard drive, SD card, microSD, whatever. Think about when you copy a file to or from one. The original file isn't moved - it stays put. The copy is moved onto whatever destinated folder you selected. That's what happened to Simon. He wasn't transferred onto the ARK, only uploaded onto it. And the dialogue after only makes it even more hard to watch. There's a bright flash, and a black screen for a moment....and then it fades back into view.
You're still in the same exact place.
Simon: "I'm still here...? I'm still here. Catherine..? Catherine?!"
Catherine (appearing onscreen) "I'm here."
Simon: "What the hell happened -- what went wrong?"
Catherine: "Nothing! They're out there, among the stars. We're here!"
Simon: "No...we were getting on the ARK, I saw it. It finished loading just before it launched."
Catherine: "Yeah, I saw."
Simon: "Then why are we still here?!"
Catherine: "Simon, I keep telling you how it works, you won't listen. You know why we're here - you were copied onto the ARK, you just didn't carry over. You lost the coin toss, we both did! Just like Simon at Omicron, just like the man who died in Toronto a hundred years ago!"
Simon: "No no no, this is bullsh*t. We came all this way, we launched the ARK!"
Catherine: "I know it sucks, but our copies are up there. Catherine and Simon are both safe on the ARK. Be happy for them!"
Simon: "Are you crazy?! We're gonna die down here, with those f**kers living it large on a spaceship! They're not us. They're not us!"
Catherine: "I'm sorry you feel that way, Simon. I'm proud of what we did. We made sure that something of hundreds of thousands of years of human history survived - that something lives on."
Simon: "No, no, no, f*ck this! F*ck this, f*ck you! F*ck you, Catherine. You lied. And I believed in you, I trusted you. You said we're getting on the f*cking ARK!"
Catherine: "We are on the ARK you idiot! I didn't lie! I can't be responsible for your goddamn ignorance, you fu-"
Catherine shorts out, due to emotional exertion, leaving Simon completely alone.
Catherine doesn't respond
Simon: "Catherine? Please don't leave me alone.."
still no response
The realization that you're completely alone, at the bottom of the ocean is incredibly sad...the only living human on Earth....the only survivor. (The other Simon is on the ARK, unaware of the stranded and alone robot Simon.)
There you have it - my thoughts on the game. It's a deep and emotional story, and is very well done. I feel so bad for Simon, being all alone, with no one else to talk to..it wouldn't be a happy situation to be in.