Oh, it gets better and better, doesn’t it. Here’s what the few lines of dialogue quoted here (and, seriously, hasn’t Bioware learnt by now to better hide the stuff in their DLC packages?) seem to say:
Millions of years ago, an organic race asked an artificial intelligence to devise a solution that would put an end to the eternal war between organics and synthetics. Because who else would you ask than an AI? And then the AI said “I’m gonna turn you all into goo and put you inside a synthetic vessel that will harvest organic lifeforms every 50,000 years” and the organic race said, sure, that makes sense. (Well, that or they had given enough power to the AI that it could enact its plan without permission, but that’s not much smarter.)
If Bioware was wickedly clever, you could imagine that the Leviathan ending would actually reveal to the player that their previous choices had all been a scam — that the AI was evil, that the first-last race had been manipulated (or altogether indoctrinated) — and you’d get new choices reflecting that new information. But I expect that, if it were the case, they would have rushed the Leviathan DLC to resolve fan outrage instead of wasting months on that free Extended Cut that didn’t change anything significant.
Damnit. Karpyshyn wasn’t a good writer (his Mass Effect books were a chore to read), but at least he understood sci-fi.