The Sadistic Choice you're forced to make in order to get to Theta. The Omnitool is broken, and you need a robot's tool chip to fix it so Catherine can pilot the zeppelin to Theta, and there are two robots in the area: one is a deranged but reasonably happy and nonviolent mockingbird, and the other is the Universal Helper, who's basically an adorable, loyal, underwater robot dog who has helped you and saved your life on multiple occasions. And if you kill the Mockingbird, the Universal Helper will become afraid of you, and you'll never see it again.
The line used in the trailers, with Catherine screaming "It's not my fault people keep killing themselves!"? That's Not Hyperbole or deflecting blame - the first Pathos-II employee scanned, Mark Sarang, had effectively started a cult that advocated for those scanned to commit suicide, so that the scan would be their "true" self from that point onward. He did his right in front of Catherine by hiding cyanide capsules in his gum, biting down after the scan was complete.
One of those that bought into Sarang's hypothesis was Robin Bass... unfortunately, you meet her just outside of Theta, which means that not only did she commit suicide, but her scan may have never actually made it into the ARK afterward - it's instead trapped in a robot pinned to the ground under the ocean. Simon doesn't have the heart to tell her the truth, allowing her to go on believing she'd made it into the ARK after all. When you later see her room, photos show her as being a fairly young woman, and she'd painted overlays on conceptual images of the ARK, obviously imagining how pleasant life inside it would be. The razor she'd used is on the blood-spattered bed, overlooked by the aforementioned images.
Then you consider that it's mentioned that WAU copied brain scans from the ARK Project to populate its robots. So that means there's two versions of Robin: one trapped in the robot, and another living her dream life in the ARK. Whether this makes it more tearjerking or not is up to you.
You can pull her plug as a way to mercy-kill her. There is no reason to do so, it is simply decided by you, if you want her to be forever stuck on the bottom of the sea alone in a dark virtual reality or if you'd rather kill her quickly. If you do the latter then she will notice that you turn her off and she screams in terror and pain, begging for her life before she fades away crying.
Meeting the very last human left on Earth, Sarah Lindwall, and turning off her life support. She thanks you and asks that you stay with her as she dies. If you do, she reminisces about her life on the surface, talks about how she wishes that she had gotten to spend her final moments with her family, and finally closes her eyes and grows silent. The life support machine shows her flatlining, and you realise that organic humanity has come to an end.
Similarly to Robin Bass, you find out earlier that Sarah was among the first to have her brain scanned. Meaning that in all likelihood, she's also living her dream life in the ARK. Again, whether it improves the situation or not is still questionable.
Finding Catherine's corpse near the end of the game. She was so close to fulfilling her dream of launching the ARK, and was seconds away from doing so when one of her coworkers murdered her in cold blood. You find her body rotting away with a caved in skull, mere meters away from the rocket she would have loaded the ARK onto. Talk about a Player Punch.
Earlier, you can read the black box of the man that killed her - he was Driven to Suicide due to what they did, though you don't know that at the time.
The ending. Though Simon and Catherine successfully upload their scans onto the ARK, the Simon we're playing as fails to realize that he himself would not be put on the ARK, a copy of him would. In despair at having been left behind, he lashes out at Catherine, who, despite her best effort to Face Death with Dignity, responds by losing her temper and cursing him for his ignorance. Suddenly she suffers a critical failure, and dies mid-sentence. Simon realizes she's gone and that he has been left all alone, deep at the bottom of the sea with no way out, forever. The game ends with Simon hopelessly begging Catherine to come back. Roll credits. At least The Stinger is happier.
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 fuckers living it large on a spaceship! They are 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 something of the hundreds of thousands of years of human history survived— that something lives on.
Simon: No, no, no, fuck this! Fuck! Fuck this, fuck you! FUCK YOU, Catherine! You lied! And I believed in you, I trusted you! You said we're getting on the FUCKING ARK!
Catherine:(getting angry) We ARE on the ARK, you IDIOT! I didn't lie! I can't responsible for your goddamn ignorance, you fucki— (the console shorts out)
While all of the fates of the employees are heartbreaking, young couple Brandon Wan and Alice Koster's are possibly the most heartbreaking and disturbing. Brandon sacrifices himself by damaging the elevator to buy Alice and his friends more time to escape from the Proxy Monsters as Alice pleads with him to come with her. Cornered by Proxies, he committed suicide by slashing his throat to avoid a grisly fate. Alice, on the other hand, wasn't so lucky. She and the group were captured by the Proxies, with her being assimilated, her entire face unrecognisable. The worst part is that she was INSIDE the train, meaning she was so close to escaping. You find her still very much alive, and speaking, with lines like "Brandon... protect me...". This is all made even worse by the simulation of the two of them earlier in the game and their messages in Brandon's room, showing how deeply they cared for each other.
In Upsilon, Simon can stumble on transcriptions of some of the last surface messages Pathos-II received before the world ended. All of them showed how much the crew's contacts in Carthage Industries commended their efforts and wished them well, but also how said contacts made an effort to Face Death with Dignity, knowing fully well that they were all doomed to die. What takes the cake though is the last transmission from Cadiz, Spain received less than a minute before impact.
Jonsy,
I know you have a much better chance for survival, but we have the better view.
Salud!
The CURIE and its crew dared to explore what remained of Earth after the impact in the hopes of finding survivors, only to find nothing but death and ruin. Unfortunately, they all died just as they were about to return to Pathos-II.
It's revealed that despite David Munshi's best efforts and the scan data in 2015, the original Simon died little over a month after said scan was taken. A dying Simon even confides to David that he's more than willing to allow his scan to outlast him, eventually becoming a legacy scan that would serve as a template for future AI.
Simon: You know what sucks about dying? The crash. Everything up till now. The brain damage, you guys, everything — it has made my life so much more... real. I started thinking about all the things I was going to do. I'd never been more excited to be alive! All that hope...wasted.
Once you get to Omicron, you need to find components to transfer Simon into a new body wearing a Power Suit, so he and Catherine can go down to Tau and Phi without being crushed by the pressure. So you get everything you need and transfer Simon's brain onto the Power Suit. Great! So everything's fine, right? Except that the procedure doesn't transfer your consciousness onto another body, it copies it onto it. You're now playing as Simon's copy inhabiting the Power Suit, while the Simon you've been up until a few minutes ago, since you woke up in Pathos II, is sitting on the chair, still conscious and wondering why nothing seems to be happening. So now the game forces yet another Sadistic Choice on you: either pull the plug on the original Simon, the character you've played practically the entire game as, so he won't have to wake up alone yet again, or leave him in Omicron, to wake up days later and wonder why he's all alone, Catherine nowhere to be seen. Simon is reasonably upset and distressed by this, and worst of all, so is Catherine. And this is the most upset and emotional we see her in the entire game, and she sounds like she's about to cry.
Catherine Well, what do you want me to do with him?! Make friends?! Let him know that we have to leave him behind when we go into the abyss?!
This sequence makes the ending of the game even worse. Simon saw firsthand what the upload does, as well as what it doesn't, yet when the exact same thing happens when the ARK is launched he's confused and angry. Had he just paid a little more attention and thought about the implications, maybe he wouldn't have blown up at Catherine and wouldn't be all alone at the bottom of the ocean.
The fate of Nicolai Ivashkin: preserved in a monstrous half-life by the WAU, unable to leave his deathbed and unable to fully awaken. He's just conscious enough to weakly cry out for his son, but that's about it. He's clutching a photograph of his son, too... and for that extra dose of misery, consider what happened to the rest of the world and realize that Nicolai already had to outlive his child before this nightmare got started.
, with Catherine screaming "It's not my fault people keep killing themselves!"? That's Not Hyperbole or deflecting blame - the first Pathos-II employee scanned, Mark Sarang, had effectively started a cult that advocated for those scanned to commit suicide, so that the scan would be their "true" self from that point onward. He did his right in front of Catherine by hiding cyanide capsules in his gum, biting down after the scan was complete.
