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Tear Jerker: Ruby Quest
When Ruby has a flashback and finds herself being responsible of the gruesome death of Stitches is made all the more abhorrent not only when we see how deeply remorseful she is when remembered, but also that she had no control over her actions, and in fact, intended to talk with him, pleased to see him looking so well (as he was at the time).
Bella was the only one whom the infection has passed over, so if she dies, she dies for good.
The fact that Bella (already horribly crippled and broken) has lived through the madness and endured the terror of the facility since its downfall; driving to the point of demanding that Ruby and Tom kill her to wake her up from "this bad dream." This made it very painful for them, as she was the only one who truly cared about them and even tried to help them all she could, even though it was against her orders. They refuse ending her life until she becomes enraged—thinking that they are cheating her by not ending her pain—ending up to her threatening them. Tom finally submits to her command and injects her bloodstream with air, killing her, and does his best to disconnect her from the life-support. He quietly apologizes for not being being able to save her.
"Moments later, Bella passes away..."
#6/ Tom Nook has been shown to fear Ace so bad—even just the mere though of him—to the point of him breaking down, cowering in a corner, and crying for his mother! Remember. This is the insane Eldritch Abomination we're talking about! It even got to the point of him completely forgetting about Lucy: his one, only, and last reason for living; and he would not even respond when she apparently tried calming him down.
Subject 6/ Tom Nook is probably the saddest example of the patients. Along with being left alone for who-knows-how-long in his filthy room and also being the most physically deformed and mutated; he seems to have almost completely either lost feeling of the unimaginable pain of his mutations and his own, indescribable smell or does not care in his desperation over his missing love "Lucy", which seems to be stronger than his own horrific state-of-being.