After all these years, I finally know that it's real and I finally know why it's so elusive.
The Apocalypse mission, in which all UFOs swarm into Mega-Primus and start tearing down the city, is triggered when you destroy the Control Chamber and cut off the stream of UFOs. It's the aliens' last act of spite.
The reason it's elusive is because usually you've wiped out the UFO fleet by then, leaving the aliens nothing to execute it with. It'll only occur if you start doing the Alien Dimension missions while there are still UFOs flying around to fight you.
I'm partway through making a mod of Apocalypse with Apoc'd. It is partially a balance mod, like karadoc's, but it comes at a lot of things from a different direction. About the only thing that's really the same in both is that Toxin A and Toxin B don't ignore shields. It also addresses the issue of some UFOs being literally worthless to research besides points, while others are completely required; the quantum physics tech tree has been massively revamped so that several different UFOs are capable of unlocking a given tech (the Mothership does have a couple of unique techs associated with it, but they're not necessary for victory).
One thing is bugging me, though: is there anyone besides me to play it? I don't see a lot of people posting in this board, and I don't really know any other boards where there's an active Apocalypse community. It feels kinda silly to keep making tweaks if no-one's going to enjoy it.
So, uh, post here if you actually want a magic9mushroom-flavour mod. Or know somewhere where I might find more people.