Sometimes Jonah tells himself that it’s just the Eye that makes him check in on Jon in his hospital bed, wanting to see why one of its most important avatars is not where he is supposed to be. Sometimes he almost believes this - but he knows it’s just him, and his…
It would be incorrect to call it infatuation, much as he desires to erase the feeling. Affection isn’t quite enough either - it would be most accurate to say that he has, rather terribly and irrevocably, fallen in love with Jonathan Sims.
This is, of course, not something he can entertain. It wasn’t something he should’ve entertained, years ago when Jon was but a fledgling under Jonah’s careful gaze. It certainly wasn’t something to continue; a breakup would’ve fuelled his paranoia, and thus his desire to find the truth. It would’ve been fitting to break up with Jon after the confrontation, allow Jon some time away from the man dedicated to hurting him in as many unique ways as he can. Spend time away from the monster who intends fully to manipulate Jon to his own ends, and use him to destroy everything. Jon would’ve realised that he deserved better than Elias, and he could still find safety and comfort in Martin, or Tim, or even some stranger off of a dating app, much as Elias disapproves of not knowing his Archivist’s choice beforehand.
But he chose to continue down this dangerous and precarious path, this path that threatens to make him destroy everything he has worked so hard for every time he sees Jon smile when he thinks nobody is looking, or hears him genuinely laugh. And Jon chose to walk it with him.