I don't think all cults getting destroyed was ever a thing, except in my long-dead overhaul of 0.4-ish. At some point in 0.8.7 or so Alien Origins were replaced with an extended list of possible alternatives, but that's about it.
Promo III is mostly the same: get Promo I, get all your NPC advisors, kill one cult (Dagon is probably easiest, or maybe BL if you have good anti-ninja techniques), and discover
something related to
one of the more extraterrestrial factions. Interrogating a
Gillman Deep One is what I usually do, but it kinda depends on what the game throws at you and how good you are at getting the right stuff out of it, especially captives.
Mansions spawn in the cities on the globe as time goes by, upgrade periodically, eat some score each month and spam hunter-killers at your non-civilian craft. And are a moderately difficult mission to kill, easier when they're young and harder when they're big and old. And the HKs also get
much worse over time. Can be cheesed like alien bases used to be, for XP and perhaps a bit of loot.
Killing the cult early enough is the primary way of handling them. Existing manors will stick around and continue being a pain (or XP farm
), but once the head honchos are gone, no new manors.