The local cops think they are dealing with a dead man come back to life because Mulder said they found his fingerprints on the lid of the coffin and also a hand print on the back of the tombstone. However it would be pretty much impossible to get fingerprints off of a stone like that, the surface is way too porous for that. See more
Mulder, these people, even when they were alive, mangled biblical prophecy to the extent that it's unrecognisable. The year 2000 is just their artificial deadline, and besides 2001 is actually the start of the new millennium.
Nobody likes a math geek, Scully.