Thread necromancy? Check.

I would recommend taking a look at how Legends of Anglerre builds organizations. I've given some thought to this myself; the conflict between organizations in a modern setting could be a lot of fun and if it's a heavy focus in the game, the benefits of statting them out and maintaining them could be well worth the effort. The core of Fate is the fractal, after all, so why not use it?

You could use scaling to build groups of enemies (or large, terrifying monsters! Haunted skyscraper? That'd be cool...). The construct (armies, big monsters) rules and the org rules in LoA seem to be mix and match as needed. Take what you see there and mutate the stunts and skills into a more modern feel.