Then, Harkness lets out an otherworldly shriek of pain and grief and launches himself at Deacon. In the small space, there’s nowhere for Deacon to go and he even if he the opportunity, Harkness’ speed far outstretches his own. The Courser catches Deacon around the throat and rams him into the cinderblock wall opposite the bed. His grip is tight enough that Deacon can be assured that it’s a threat against his life, but it isn’t yet enough to kill him. “You bastard,” Harkness snarls at him.
Oh man, out of all the bits... Welp, here we go. Remember you asked for this rambly mess.
So, TL;DR version is, Harkness is mad at both Deacon and himself and thus doesn’t immediately kill Deacon out of guilt. Thus giving Deacon a chance to talk himself out of death.
Basically, what I wanted to convey here was that in coming back to himself (the one that he was when he defied Zimmer and left the Institute in the first place) he has this soul-crushing realization that who he was had been taken from him and he’s had to live the last decade as a mindless slave to Zimmer. Which, is worse than it was before he has his awaking as an individual and eventually coming to disagree with the Institute’s policies of capturing and wiping escaped synths because who he was had been taken, most violently, from him.
His rage at the destruction of who he was is something that really can’t be understood by anyone who hasn’t gone through that experience and ironically is exactly what saves Deacon’s life here. Because at the same moment he realizes that his life had been stolen from him, he finally and truly understands what it was that he did to all those synths as a Courser.
Yes, he came to disagree with the practice, and thought it barbaric and wrong, but like many Railroad members, he’d never experienced it. So while he could object to being used as the Institute’s weapon of choice against his own kind and morality of their decisions, he couldn’t understand the true depth of the cruelty being afflicted on synths.
He’s well and truly inraged by what Jack had done to him, but he’s also so ashamed and horrified that he’s done the exact same thing. To dozens of synths. And yes, we can argue that he didn’t know any better for some of them, but that doesn’t make much of a difference to Harkness. He would tell himself he should’ve realized it sooner, acted faster when he first started disagreeing, instead of waiting so long to break from the Institute out of fear.
It’s that sick realization that saves Deacon’s life. If Harkness had never been a Courser, he would’ve killed Jack and not felt a moments remorse, but because he had done exactly what Jack had done, he couldn’t well go back to his own true life after killing someone who (in his eyes) had committed less of a crime than Harkness himself.
Jack only set back one synth. Harkness, many more than that. And unlike Harkness, he had become a member of the Railroad and was now helping other synths. Harkness himself didn’t take that risk, instead choosing to become totally anonymous. He said it was to keep the Institue off his tail, and it probably was to some extent, but the Institute also instills a lot of fear in its creations, and Harkness was likely too afraid to risk his own life, let alone the lives of any Railroad members should they all be caught out.
But after seeing the lengths Deacon went through to be invisible to the Institute, to the Capital, to everyone, he is ashamed he didn’t think to do the same.
So yeah. Guilt keeps Deacon alive and kicking, and Harkness has to learn to live with himself.
