The Rambaldi device (referred to as Mueller, sp?) was mentioned as possibly being used for good or evil. This one just happened to be used for evil. The third Derevko sister, Elena (Sonia Braga) has been the mastermind behind various terrorist cells and Rambaldi plots for the past five years, apparently.
She used mind-cloning technology and a look-a-like to make Jack Bristow think he killed his ex-wife, Irina Derevko, in an effort to protect his Sydney.
She also spiked the water supply of this Russian town (and many other strategic locations around the world) so that when the big red ball was activated, it would make people become embodiments of aggression.
As far as the message on the mountain is concerned, I can't remember exactly what was said. But I don't believe it really illuminated that much, and when it was revealed, it was a bit of a letdown. The secrets never quite pay off when they're revealed in Alias. Even this apocolyptic situation, with accents of "28 Days Later," felt hollow and empty.