I decided to buy a "The Skulls" collectors edition DVD that claimed to include "The Skulls: Initiation"
Bad news. I decided to buy "The Skulls" Collectors edition DVD. I thought that it might have had some offline version of "The Skulls: Initiation" project as one of its DVD-ROM features, given the article and sources. There is an "install" option, but it just installs the "PCFriendly" browser. This browser then attempts to load the Universal site. As far as I can tell, no actual assets from The Skulls: Initiation were bundled with the DVD. Given that the WayBack Machine wasn't able to archive the live site, it looks like this game is lost forever, unless someone from the project kept a copy.