The moment when Sam finds the brains connected to the A.I.. Also serves as The Reveal.
Sam: "Please don't let me find you... ......oh."
The distress in her voice is heartbreaking as she begs you to not be in the situation that she fears you're in. Her pleas are in vain.
What's worse is that the player will probably realize the situation in the same moment as Sam does, making it even more impactful.
The price for compiling the Antivirus is permanently damaging the ship that you and Sam are in. The music instantly becomes quiet and sad as Sam begins panicking. The system announcer again and again updates that Sam's chances of survival are going lower and lower. And then there is only one message by the system left:
Chance of host survival 0%. I am sorry.
In the end all that Alex can do is scream and either tell her they'll meet again or beg her to stay together, only to be send off to Oriens station.
And then the beautiful song "Covers" by Lena Westermann starts playing as the title screen shows Alex being send through the network, leaving Sam behind.
One of the brains that Sam can save is Patu's. Which means it crashed together with Sam. So no matter how that decision plays out, if you chose his, he's dead.
As much as Colburn is a hateable character, it is difficult to not at least feel a tiny bit of sympathy for him when he sits crying in the corner of the human test subject lab after having seen his dead daughter in one of the scenarios or hearing him talk about Lilly getting thinner or about her death in the audio logs. While it doesn't justify his actions, it serves at least as means for understanding most of his motivation.
The travel to the satellite station to upload the anti-virus for Code 7? All for nothing. It's actually Code 7 itself you've just uploaded. The helper program that's aided you in your journey? It's actually S.O.L.I. And even worse? Zoya dies believing you betrayed her and all of humanity.