I've been running a Delta Green game set in the early 1960s. So DG is still technically legal; they're just so secret and undercover that they don't have "call in an airstrike" resources. I have the general premise, but my biggest problem is that I haven't figured out what the Big Secret Plan at the end is.
Essentially, I've got two mythos factions that the players should get caught between. The Anasazi are barely-refluffed Serpent People: an ancient race of sorcerer-priests who ruled some of the pre-Columbian civilizations in the Americas, and since then have been infiltrating government and industry. They're evil cultists--blood magic, all that jazz--but they generally prefer the status quo, ruling the humans behind the scenes.
On the other side are the Mi-Go and MJ-12, with the full force of the Cold War arms race behind them. My idea is that the Mi-Go are developing some kind of Big Bad Apocalyptic Event using all the industrial resources at their disposal. The Anasazi want to stop this, but their methods involve all kinds of morally-reprehensible sorcery. So the investigators may have to walk a tightrope between helping evil cultists, and fighting evil aliens.
My biggest problem at the moment is that I haven't thought of what form the Big Bad Apocalyptic Event should be. I suppose I could just rip off Divine Fire and make it a not-a-nuclear-reactor that summons Elder Gods. But I keep thinking there should be more to it than that. Something more complicated than "this is the machine that causes the End Times. Blow up this machine."
On a different note, I have one PC who was crippled in the first couple sessions; I'm planning on giving him a "how would you like to walk again" deal with some sort of Bad Thing. Not really sure what sort of consequences I'm going to throw at him if he accepts, though.
So anyway, any sort of wild-ass theories or general spitballing would be helpful.