There’s a different Season 4 out there where Jon, desperate to find proof that being a Fully Fledged Avatar that Eats People Trauma can still, somehow, be good in some fashion, doesn’t find Fanshawe’s letter first and therefore immediately concludes, with no shred of doubt (and with endless self-loathing because he’s mirroring, his boyfriend is ghosting him, nobody is happy he’s back, and he’s like few episodes away from jumping in a coffin being like ‘eh, it ever works or i die’) that Jonah Magnus was an evil man all along and there was never anything good to the Institute.
Maybe instead of he finds a letter from Jonah to Smirke that tells the fall of yet another of their friends, maybe a letter that, on paper, is perfectly polite, but that Jon reads with the undertone of anger and fear (you said balance is the key but prevention is doing nothing we need more knowledge, we need to understand more, Robert-). Maybe, if we want to keep it at “we never hear from Jonah directly” (which does also have sexy implications, find) he finds a letter from yet another friend who actually recalls WHAT happened the day Smirke told his buddies about all this, that shows that Jonah immediately was with Smirke on the whole “balance thing”, at least on paper.
In any case, what he finds is not a downright “oh, Jonah bad” and Jon wants to believe SO badly that he can still do some good; also he’s obsessive and doesn’t know when to quit, as we know <3 so he just keeps. finding new letters to read, which, of course, parallels his own journey, and so, of course, when we reach the final, actual reveal of Elias being Jonah, it’s just. oh. Oh.
(Side note: got distracted by the end of this post because I was reminded again that, genuinely, when this podcast is good it’s brillant, and Elias going “Exactly where they’ve always been, Martin. Watching over my institute.” is just. so. fucking good. what a delicious, perfect, satisfying reveal. I adore him so much. It’s just so perfectly dramatic. that whole scene!! THat whole episode. god. anyway. what was i saying? i don’t remember)