The Mi-Go in Delta Green experiment on humanity. They don't want to kill us all. We make good lab rats.
The point is a good one, though I suppose using phrases like "apocalyptic event" oversimplified things. I'm not going for a "and then they killed us all" kind of plot, just some kind of really big event that nobody wants to see happen. Like all of America getting stuffed into Matrix-tubes to serve as a giant intuition-computer for the Mi-go, or Missouri getting turned into one big, festering portal/spawning pit. Stepford towns filled with telepathic grub-parasite victims. Or something.
As to whether that's too overt for the Mi-Go...well, fuggit. Nobody in my group is so in-depth to the mythos that they're going to start shouting THEY WOULDN'T DO THAT. And besides, this is the 60s rather than the 90s--plenty of rationalizations to be made for the Mi-Go having attempted a more big-picture project back then. Maybe its potential failure is what causes them to tighten up security and go deeper underground, etc.
For this game, I'm a bit attached to the Mi-Go and MJ-12 because I want the players to have that moment where they realize (even though they're still "legal") that they are not the big boys from the government, here to kick ass and call in an airstrike. The big boys are actively working for the other side.