I don't know if it's going to be d20 Modern or not, but there will apparently be a d20 version of Bureau 13 in a few months.
Bureau 13, aka "Stalking the Night Fantastic" was probably the first game in this vein first showing up in the early 80s. The players worked for a super-secret government agency which covered up paranormal incidents (because paranormal incidents tend to cause others when they get widely reported, which can cause problems, like the Monkeyman of India a couple years ago).
When I first heard about the show the X-files, I thought it was a rip-off of Bureau 13 (especially since B13 actually had the term 'X-file' in it, although with a different meaning).
Not quite, but there are a lot of similarities. B13 is also one of the few games that can be really funny at times, like the X-files would occasionally be funny.
The author also really knew a lot about the paranormal. Most of the later games are written by poseurs or skeptics, and that loses quite a bit of the mood. Sort of like John Tesh singing a rap song.
There's also going to be a d20 version of Chill, which was another early horror game. No conspiracies, really, it's more like Poltergeist: The Legacy. But worth mentioning.