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There's a chance for a belted happy ending.
If the first Simon and WAU survive, together they have a chance of reviving humanity in a physical form. The Simon's could keep each other going until they either use the WAU's technology or find a way to work with it, and upload the ARK scan to proper bodies to rebuild civilization.

Variation on the above chance for a belted happy ending... Simon builds a robot civilization
It would require an incredibly strong constitution, and patience, to keep from going insane, and plummeting past the dispair event horizon.

The thing is, a lot of those robots have human personalities, and they can be repaired. Simon and others can also replicate their personalities ad-infinum. They’re automatically better equipped to survive New Earth. If they can get to the point where they can mass produce future robots, they could expand without biological limitations, and pick up where humanity left off.

Rather than try to biologically recreate humans, they could design androids, which are less susceptible to environmental changes. It would be a completely different way of life, but the phoenix rising from the ashes would be muuuuch more resilient.

SOMA is set in an alternate reality or perhaps the extremely distant past of Eclipse Phase.
The details change but the core points remain. Humanity has brain-scanning technology that copies personalities and sleeves them into new Morphs. Simon spends the game in several Synthmorphs while Catherine stays an Infolife. The WAU is similar to a proto-TITAN, even developing its own strain of the Exsurgent Nanovirus with the Structure Gel that infects ocean life and drives people mad. Humanity as a whole suffers a 'Fall', and is reduced to Infolifes who orbit the sun, potentially escaping their confinement and rebuilding as a Transhuman culture.
Whatever is attacking the research base compels its hosts to kill themselves so that it can transfer consciousness to the machines.
From the Theta teaser, we know that researchers have been committing suicide, and in the gameplay trailer, we see one such victim in close proximity to his machine double. Maybe whatever is attacking the base (perhaps what the researchers were studying) cannot retain full consciousness at the same time as its biological double, and so compels them to kill themselves by some means.
  • Jossed - the reason for the suicides is actually due to an Apocalypse Cult that sprang up around the ARK's existence, with the leader, Mark Sarang, claiming that the only way to make the Brain Uploading "real" is to eliminate the body just after scanning, to preserve the stream of consciousness.
His brain was uploaded to a machine, but crucially he still thinks he is flesh-and-blood. It is already established that those who have been uploaded see themselves as being no different than what they were before, and the Player Character is not exempt from that. There will be a Tomato in the Mirror moment late in the game where he will have his Robotic Reveal.
  • The only possible hole in this theory is that we are able to see other robots are actually robots, even if they are unaware of it themselves. Which means if the talking, friendly robot sees us as a human, we might actually be human. At least, on the surface... And then again, the friendly talking robo-Carl says we do look kind of "messed-up." Hmm...
  • On the other side of this, though, Robo-Carl also seems like he recognizes Simon, though Simon doesn't seem to recall ever meeting the real life Carl. When Simon clarifies that he doesn't know what's going on, Robo-Carl amends that Simon must be "new." This plays into the "Mockingbird" teaser which showcased that humanist robots will rationalize away inconsistencies in their worldviews. Much like people.
  • Played with: up until meeting Catherine Chen, Simon believes he's flesh and blood, but is disabused of it when he survives being flooded without having put on a dive suit, as he actually is a dive-suit. The fact that his brain was scanned in 2015 and the year is now 2104 is an early giveaway.
Given the motifs here, it wouldn't be much of a twist to just have the player be a secret robot. Think Shutter Island. The real twist? Not only is he a secret robot, but he knew that the whole time. The story just never saw fit to reveal it to you until right then.
  • Jossed: This secret is revealed to both Simon and the player when they meet Catherine Chun on Lambda station.
Simon Jarett is perfectly human.
The PC is human, despite the visual glitching and the other overt themes implying, but is amnesiac for some reason. There will be no twist regarding the PC's humanity, just the humanity of everyone else.
  • Jossed: It's not even a big secret that Simon is a digital recreation of someone uploaded into an advanced diving suit. He isn't even freaked out to realize that, reasoning that he might as well be the original in a more mechanical body. And doubly Jossed, as the question of humanity is even more ambiguous for him than other ARK bots; Simon is the only robot not a copy of an organic individual.
    • What makes Simon not "an organic individual"? He was a regular guy working in a bookstore in Toronto. It doesn't get much more organic. His personality scan wasn't made for the ARK, but that's more or less the only difference.
    • Catherine says that Simon is an "A.I. template" used by programmers in the future, based on the brain scan of the Simon Jarret from 2015. The others are direct copies of people's minds.

Near the end of the game, choosing to destroy WAU is not the best choice
The actions taken by WAU to ensure survival of the little that's left of humanity have certainly led to horrific results. However, it was gradually getting better at it: from mindless, zombie-like creatures, to putting mind backups in robots, to finally creatures like Ross (similar to the "zombies" but keeping enough sentience to want WAU destroyed) and Simon, a fusion of human and robotic parts that was ultimately capable of bringing WAU down. So what if, through attempts and with the memory backups, WAU ultimately managed to create "new" humans capable of surviving on the destroyed surface of Earth, and kickstart a new beginning for our race? Think of the alternative: The ARK is sure to make the legacy of humanity live on, but will it ever be able to communicate with the exterior of the satellite? Won't it become an immutable virtual cage?

"Continuity" is real.
At the very end of the game we get to play the Simon that got on the ARK, but only after having seen how the one still left on Earth reacts. Could it be that the reason we get to see the ARK is because the Simon still on Phi might have killed himself while the credits rolled, after being left alone by Catherine?
  • Jossed. How would you explain what happens at Site Omicron, where the second Simon clearly has his own independent existence? More importantly, if "Continuity" is real, what would happen if someone activated a scan in a simulation outside of the ARK?
    • This goes into metaphysics but it's not like the game doesn't delve a bit into that... Now, if consciousness is an entity that transcends the body, as Sarang proposes, making it not unlike the religious concept of a soul, "continuity" would be a convergence of a consciousness whose body has died, with a 'living' copy, which is why believers kill themselves once they have had their brains scanned: in order to "continue", i.e. rejoin their scans. Apparently, it would be necessary that the death be chronologically close to the scanning, as evidenced by the mockingbirds not recalling their deaths. That would explain the independent existence of the living copy, and that of the first Simon, if left alive. If killed, it might be that he "continues", but, of course, we will never know that. If someone activates a scan outside of the ARK, that scan is simply a copy and does not necessarily "continue", for as long as it is arguably "alive". Finally, that could explain the fact that we can play the third Simon, the one in the ARK, if the second Simon kills himself in his grief.

"Continuity" exists but isn't some psudeoscientific conciousness thing.
Let me open with an example. In one of the revelation space books a man hires an assassin to attempt to kill him with a poison that acts over the course of around a decade if I remember correctly. He does this because his uploaded family have been pressuring him to join them in a virtual world for a while. He took issues with the fact that there would be multiple versions of himself running around (obvious he wasn't a programmer, redundancy and back-up are important) so he set up the assassination contest to force himself to pick one existence. when he gets hit with the poison dart and has his lifespan cut down to ten(maybe) years he goes off to get the scan. With this in mind, he is not leaving anything behind and his uploaded self will be free of the worry for his flesh and blood self. It kind of similar to the method of teleportation that makes a clone at the destination and kills the original. Considering all this the suicide cult makes more sense, the cult members wanted to be the only "Them" in the world and killing off their wetware selves solved that particular issue, especially since said wetware was happy to do so. In the end, it all comes down to personal ethics and the concept of the self, just something to think on Tropers.-Analt

Ross does not exist...Sort of.
Ross blatantly disregards most laws of physics, teleportation without massive reserves of power and equipment being the most egregious sin. I propose that Ross is not actually a physical entity and in fact an attempt by the WAU to mimic the Arcs virtual world technology. Ross now exists as a sentient brain scan but instead of being stuck in a cortex chip he can upload himself into the structure gel based systems of the complex. He simply manifests a physical image of himself into anyone's field of vision. It also explains his insanity and early attempts to murder Simon, the systems he's uploaded himself to can't properly run his brain scan and so he lashes out at everyone else blindly. It also explains why your vision messes up when he shows up, he doesn't have an EMP like the other monsters, he's over-taxing the system Simon is running on.-Analt

  • Possibly half-right. Ross very likely does not possess the ability to teleport, but it is unlikely that he does not have any physical presence at all. How else would you explain him being devoured by one of the WAU's creatures near the end of the game? What he might have, however, is the ability to screw with machines, such that he could render himself effectively invisible, manipulate them from a distance, or communicate without being in the same room as Simon.

The structure gel was made with technology reverse engineered from the Engineer.

The Earth of Soma already has slightly more advanced technology than we do in 2015, particularly in neural imaging if the WAU was able to build a mental clone off of a somewhat invasive medical scan. At some point someone was able to find the remnants of Mandus' would be mechanical god and figure out how it was able to make the pig men, and from there create a new machine god without a human soul to power and direct it.

If this is true, it makes the fundamental tragedy of Mandus even greater: the fact it was a comet and not World War 3 that did organics in, with the WAU's fundamental inhumanity making it far more of a problem than any misguided and panicked scientist, means that his viewpoint was just plain wrong.

well, now the serious stuff is out of the way, how about something silly?

Soma is a prequel for Splatoon.

Wasn't part of the background story for Splatoon that all life on land was destroyed by a meteorite (yes I know it's different from a comet, but still, it's a ball of solid mass from space) and thus given the sea creatures a chance to evolve and rise from the ocean? Seeing how the squid population had a sharp increase shortly after the impact I'd say it's more likely than you think. Hell, maybe it's even the structure gel that gave the cephalopods the ability to shape-shift.

  • Wasn't a meteorite that destroyed life on land, it was rising sea levels.

Simon is actually a Timelord.
Now I know how it sounds, but just think about it! How did Simon survive all those years? Time travel! How does he keep living through dieing to things? Regeneration! How does the omnitool interface with everything? Sonic screwdriver! How does Ross teleport and stuff? He's an alien! How does the WAU think that torturing everyone is an acceptable means of preserving humanity? IT'S A DALEK OR SOMETHING!

...

Okay okay enough of that... all joking aside a post launch facility with the WAU still active would make a great premise for an episode though. The Doctor gets a distress signal, lands onsite, discovers the WAU and Simon (Both Simons?), pulls something out of his arse like the human brain still remembers how its body is built and still has all the necessary DNA to rebuild, removes the structure gel from the wildlife and then hands over the secret to terraforming the earth back to normal again...

And then a skeleton popped out.

There will be sequel in which Simon tries to find the remaining human beings in space.
It turns out that the underwater facility is not the last vestige of humanity after all. Remember: it was used as a facility to launch spacecraft into space, which could easily have had people on board. So there could be people living in space stations orbiting the earth, unaffected by the comet's impact, or maybe even on the Moon or Mars.
  • There were logs in the station that documented only satellites being sent into orbit with the Omega Space Gun. In addition to the compartment of the "bullet" being very small (only big enough to send maybe a single person at a time), the squishiness of a human might be a limiting factor when being launched into space via rail-gun without significant recalibration (assuming such adjustments wouldn't eliminate the ability to reach escape velocity). It might be possible for a cybernetic/robotic being like Simon to achieve, but it's unlikely there is an unknown colony in the stars... It does beg the question, however, what was the state of the International Space Station when the comet hit? If a company could span across the depths of the ocean floor, would there not have been advancements made in space travel and colonization?

The ARK is actually an interstellar spacecraft.
Because it would be kind of short-sighted to just launch it up there and wait for it to break, right? A Bussard ramjet is within our capabilities as of 2015 - it would just be limited to something the size of the ARK. It would take thousands of years to reach another star, but nuclear batteries can last that long easily, and mind copies don't age. Besides, the final shot is of the ARK firing some kind of rockets and the ruined Earth panning out of view as the ARK zooms into the distance...
  • An in-game schematic reveals that the arc is designed to orbit the Sun between Earth and Venus, anything beyond those orbits is marked as unsurvivable.

DLC will give us Simon versus Simon.
Players will take control of the copy of Simon left behind at Site Omicron (Simon 2.0), lost and confused by Catherine's disappearance. The antagonist, meanwhile, will be a combination of the WAU and Simon 3.0 (most likely reusing Jin Yoshida's enemy model), now sharing a desperate desire to "restore" humanity.
  • Considering the nature of SOMA, players will have the option of jumping straight into the DLC or branching off to it at the appropriate moment while playing the main game (either by checking a box at the starting menu or tying it into the player's choice to kill or spare Simon 2.0).

The reason that the WAU tries to stop Simon and Catherine sending out the Ark is because of what the Continuity cult did as a result of it
Logically, there shouldn't be any reason for the WAU to impede Simon and Catherine from sending the ARK out, and in fact should assist its development, given that it's a long term way to preserve humanity similar to the drones it creates. However, given that Mark Sarang and his cult all killed themselves after scanning their brains onto the Ark, the WAU likely determined that the ARK was a detriment to the survival of humanity and sought to prevent its execution.

It's not a coincidence the same voice actress voices both Ashley and Sarah
The similar-sounding voice is symbolic of how Simon's life experiences inform his empathy towards others while he's at the increasingly crumbling Pathos-II. As a consequence of this, and the questionable accuracy of Simon's pre-scan and post-scan mind, there's a bit of a blur between Ashley and Sarah in Simon's perception. Simon's memories of Ashley's voice might even be misremembered, with his mind retroactively conflating the sound of her voice with the sound of Sarah's voice. If the player opts to stay by Sarah's side until the bitter end, it's not just a simple humane gesture by Simon, timid gentleman that he is. By doing this, he's also consciously parting with his own past, knowing there is no way back for either him, or the rest of humanity.

The WAU had tempted him earlier with a fake, unconvincing dream about a happy life with Ashley, so Simon decides to defy the bottled-up grief he's held over Ashley's death and funeral by letting go of the past and focusing on finishing his mission. Deep inside, he might feel guilt over not being able to prevent Ashley's death, as hinted in his waking nightmare, and not being able to say goodbye. By doing everything in his power to help Sarah in her suffering, he gets one final chance to free himself of that sense of guilt. All the more symbolic, given that Sarah's the last real human being left, and the very last woman. Simon might feel he had failed Ashley, but he's not going to fail the equally suffering Sarah.

Related to that, the friendship between Simon's and Catherine's simulations after the successful launch of the Ark might actually end up strained. Despite all the tough stuff they've been through and the sense of camaraderie they developed as a result, Simon's discomfort with some of Catherine's more pragmatic attitudes might drive a wedge between them. In the long run, Simon might end up being closer to Sarah. Purely because he doesn't have experiences with her that were as morally ambiguous as those with Catherine, and because his interactions with the real Sarah were one of the few genuinely human interactions he experienced at Pathos-II. Most of his interactions were with long-dead or dying bodies, so talking with and showing empathy to a still conscious human like Sarah probably felt like a godsend to Simon, even if the circumstances of that meeting were incredibly sad. This has a somewhat darker implication, though: Simon might view the ARK Sarah in an idealised light, since he never experienced anything other than her NiceGirl side of the real, suffering Sarah. She might even remind him of Ashley. Whereas with Catherine, he saw both the wonderful and less pleasant sides of her personality, for better or worse.

Are there two copies of Catherine on the ARK?
Throughout the game we learn that Catherine uploaded herself to the ARK together with the rest of Pathos-II crew. However, at the end of game, she transfers both Simon's and her own scan. Does that mean that there are now two Catherines on the ARK, each with slightly different memories?

SOMA takes place in the same universe as Penumbra...
...and the comet, Telos, contained a successor to the Tuurngait. It attempted to infect the WAU and they merged, which is what gives the WAU the power to infect entities and use them as proxies, just like the Tuurngait. I have no proof for this, but the random mention of "have you ever been to Greenland?" late in the game is weirdly specific.

Simon deliberately caused the car crash.
It's painfully obvious his crush on her was hopeless and nerdy guys form a sizable portion of the 'incel' community, who often react violently to rejection.
  • The accident was caused by another distracted driver running a red light. Besides that, we've seen Simon lose his temper; while he can swear up a storm, he's never threatened anyone or reacted violently.

The ARK got hit by an asteroid minutes after it's departure
Because why not.

There IS a transfer
The copy is actually the one that gets left behind as a form of residual data. However, this actually manages to make the situation more horrifying because it actually works from beyond the grave. That's right, people are yanked back to "Life" so that they may suffer.

The WAU is an M-rated counterpart to AUTO from WALL•E.
Both stories have a devastated Earth, robot protagonists, an attempt to flee to a paradise among the stars, and an AI villain whose prime directive is to "preserve" human life at all costs with no regard for human free will. The WAU's narrative arc is much darker because unlike AUTO, the WAU is not defeated early and thus is able to follow through with all the implications of what "preserving" human life over human objections might look like.

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