Official? Not to my knowledge, and I've looked.
Conspiracy genre games were moderately popular in the mid to late 90's though, and the best one (IMHO) was Dark*Matter, which was WotC's entry into the field with the Alternity system in 1999. It was discontinued when 3e came out so WotC could switch to only producing d20 games.
It also has the easy side benefit that it was mined heavily for ideas for d20 Modern (the d20 Modern Menace Manual has many creatures and organizations from that setting), and you should be able to find the books for the setting pretty easily on eBay, and I think they are (or were) sold as ESD. There was also a Dark*Matter mini-game in one of the last issues of Dungeon/Polyhedron. Even if you aren't interested in the setting per-se, d20 Modern (especially with the Menace Manual) have plenty of Greys, interdimensional abominations, cults & conspiracies, black helicopters and urban legend creatures for an X-Files type campaign (including at least some rules for playing FBI agents).