Well, apparently he checked himself in for a 30-day rehabilitation - I take it the last few years haven't been too kind to him. But if there's anybody that can tell us about the Millennium Group, it's him. He used to consult for them. Later, he fought to bring them down at the expense of his own career and reputation.
Mulder, those people, even when they were alive mangled biblical prophecy to the extent that it's unrecognizable. The year 2000 is just their artificial deadline - and besides, 2001 is actually the start of the new millennium.
[Mulder and Scully are watching the New Year's celebrations on TV, which is showing kissing couples and everyone celebrating. They look a little awkward. Both turn to look at each other, then lean close and kiss gently for a few seconds, then smile.]