The second fallout was the transformation of medicine and medical technologies due to the confirmation of epigenetics as a thing. Once that became known as a thing that could significantly transform an individual due to psychological factors, that got suppressed by the governments worldwide right away; they wanted super-soldiers that they controlled, and not free superhumans doing as they like. Epyon wasn't having it; he organized his nascent department to break this information loose, and they did- and without Control saying so. The results were that this too soon got online and embedded into the Darknet, making it impossible to erradicate without destroying the Internet worldwide- a thing that was never going to happen.
The combination of cheap power soon turned into cheap and good Internet access worldwide. That undermined corporate and government centralization through the proliferation of things like easy 3d printing and other technologies of that sort. The Agency picked up on this trend early and used it to our advantage to exert leverage against the enemy organizations we discovered, mapping out and rolling them up in turn- but far more quiet and with far less fanfare. By the time I became Control, Epyon and the other super-soldiers we recruited worked to transform the world into a place I once believed only could ever exist in the more hopeful of science fiction stories.
More than that, I can't say for certain. Once I retired from the Game, and Epyon took over as Control, the Agency had become a true peacemaking organization. Sure, the shadow aspect remained; there remained a need for things done discreetly, and early intervention often nipped problems in the bud well before the super-soldiers became necessary, so the only real thing to worry about now was the possibility of infiltration, either by enemy actors or (more likely) complacency and decadence.
But that's another story.