Admins for the site gave clues and fans worked with those clues to discover user names and passcodes to open locked sites. Each site almost invariably led to another. There was supposed to be a cartoon featuring the Ghost Children, the otherworldly fans of Glass and the Machines of God, the fictional alter-ego band of the Smashing Pumpkins. However, only about 20 minutes of the cartoon was ever released, in its unfinished form, before the project was dropped.
The whole mystery seemed to just fizzle out with the band, especially once Billy Corgan became preoccupied with Zwan, another musical project. It is a very difficult and convuluted thing to explain. The mystery was something that needs to be experienced to be understood.