According to the Freemason's calendar it will occur in the year 2000, and indeed it will."
Cooper seems to be generally "right on", however his last bit, claiming that the star would appear again, obviously turned out to not be true. I have looked (extensively) and not found anything in any official Masonic writings on the subject referring to this prophecy, or the Calendar supposedly being oriented to the year 2000 for this purpose, so maybe he made that up or got it from a spurious conspiracy source.
Another website offers more on the Vela stellar explosion, and also contains stuff from Sitchin about how it impacted the Sumerian culture:
What Cooper was referring to that didn't happen in 2000 was Project Lucifer.