The prophecy begins by saying "the second thousand will still be new," referring to the second millennium (a thousand years). The "first thousand" would have been from years 0 through 999, and the "second thousand" from 1000 through 1999. The year 2000 marked the start of the third millennium. If he were actually talking about the second thousand, it wouldn't have anything to do with these events since the episode aired in 2001.