On the one hand I feel like Jon would proooobably have already discovered his rape kink well before starting at the institute, but Consider:

It’s S2. He’s terrified that everyone around him wants to kill him. He Knows there are monsters that definitely want to kill him, but there’s perfectly human monsters too just like whoever killed Gertrude.

And maybe it’s an idle thought, at first. Elias sees him in the morning during a meeting, asks if he wants a cup of coffee, and Jon wonders what if he slipped something in there? He didn’t. He wouldn’t. Would he? How would Jon know? What if he did? Worries about it the rest of the meeting. And with Elias droning on about next months budgetary allocations it’s all too easy to expand on it… Elias slipping something in his drink to make Jon loose and pliant and unable to fight back as he slides down his trousers. Teasing Jon for how wet he already is. Pushing deep inside with a satisfied groan, the pain of the stretch and the terror of the violation not enough to distract from how good it feels when Elias begins to thrust, reaches down to play with Jon’s cock while his other hand gropes his tits. He’s going to breed Jon. He’s going to pump Jon’s womb full of his cum, and he’s going to make sure Jon enjoys it. Maybe he even does it in front of the other attendees, watching silently as Elias rapes and breeds his prickly, temperamental employee over the table, Jon drugged and helpless and unable to stop himself from moaning in pleasure.

Jon is ashamed to discover how wet he is, how easily the idea came to him and what it did to him. And it follows him for the rest of the day, thighs clenching and cunt leaking and face a tiny bit flushed, too distracted to focus on his work. It plagues him on the tube ride home. Mixes with the fear that he’s been followed. Elias is probably stronger than him, after all. What if he just follows Jon, corners him somewhere dark and hidden, forces him up against a wall and yanks down his trousers? Forces his cock inside without any preparation as he roughly pounds Jon. Degrades him for how wet he got, his little moans, how much he’s obviously enjoying himself, how much he likes this.

Jon all but sprints back to his flat, doesn’t even make it to the bed. Just stumbles over to the sofa and ruts desperately against a pillow until he cums in his pants.

He has no idea why the idea is so affecting. It’s terrifying, obviously. He’s so, so afraid. But there’s something about the violation and the loss of control that just gets him utterly soaked now.