The last Major Plot Thing that happened before the game's untimely end, as I recall, was the Magisterium trial. I recently did the Provost Marchand stuff that was in I24, and it reminds me that I want to make sure I know what happened to everyone. Keep in mind, when I say "what happened," I don't mean "what officially happened as far as our characters know," I mean "what do we, as players, know happened." I did all of the Incarnate Trial stuff back on live, but that was ten years ago, and the wiki doesn't consolidate any of this information.
So, going down the list on the wiki in alphabetical order, then...
Anti-Matter: Officially unknown, but he sacrificed himself to get Metronome to the space station.
Battle Maiden: I think she was captured during one of the Incarnate Trials? But I am unsure.
Black Swan: I have no idea. Killed during Magisterium when Cole nuked it, maybe?
Bobcat: Captured, awaiting trial. This is brought up in the Provost Marchand storyline, in which they say she is dangerous, but not actively a threat. They don't say it's because she's lazy and dumb, but c'mon man.
Chimera: I think he was killed during the Magisterium trial.
Diabolique: Getting rid of her is the entire point of the Dilemma Diabolique trial.
Dominatrix: Captured, awaiting trial. As per the Provost Marchand stuff once again, her help during the Dark Astoria stuff will buy her some leniency, but she's a scheming backstabber so they're worried about what angle she's working.
Infernal: No idea.
Malaise: He was pretty important during Minds of Mayhem. I don't know his fate in the wake of that, but I wouldn't be surprised if most of who he was is basically gone after Mother Mayhem used him as a fallback point.
Marauder: As of the end of I23, basically depowered because Neuron is a sloppy moron. There's more to it, but that's a huge part of the Provost Marchand stuff, and since this is specifically about the game as it was at shutdown, I'll leave it at that.
Mother Mayhem: Killed during Minds of Mayhem.
Neuron: Officially unknown, but he tried sacrificing Bobcat while he escaped the Devouring Earth. She took this poorly and killed him. I think I read this on the forums or some other "official but not in-game" type source.
Nightstar: I'm pretty sure she's dead in the wake of the Behavioral Adjustment Facility trial.
Shadow Hunter: Officially unknown, but he's encountered in some of Number Six's missions, which did not exist on live at the time. I think what it shakes out to is "he got Devoured and now you have to put him down."
Siege: I'm pretty sure he's also dead in the wake of the Behavioral Adjustment Facility trial.
Tyrant: Captured, awaiting trial. I know that there were plans that basically shook out to "we need a figurehead, Statesman would be perfect but he's dead, fill in for your Primal counterpart and we'll take that into consideration while dealing with your many horrible war crimes," but I am unsure as to the status of those. Mostly because the only reason I know this at all is because that's what was going on with Statesman's appearance in Master X Master, NCSoft's MOBA.
I think that's all of them? As you can see, I remember most of them, but the wiki does not put everything into one tidy "here's the deal" pile.