The Catalyst. You have an AI that was created to facilitate communication between organics and synthetics, but something went wrong with its original programming, resulting in it going mad and deciding that conflict is inevitable, and that therefore the only option is to destroy its creators, thereby coming to embody the very problem it was trying to prevent, and now it has been stuck carrying out an extremely perverted and twisted version of its prime directive for millions of years. It could actually be a pretty interesting, if archetypal, Sci-Fi story in and of itself to explore, and play into exactly the kind of cyclical structure of past generations' mistakes coming back to haunt future generations the game seemed to be trying to create. The problem is that all of it is awkwardly dumped on the player literally in the last 10 minutes of the game (though the Leviathan DLC addresses the problem a little bit) and it is never actually explored; there is no option to tell the Catalyst that it might be insane and what it is doing is absurd, as the player is not allowed an option, even in the Refuse ending, to actually discuss the logic (or the lack there of) in its actions.