Great Khanate
The Great Khanate (1988-1996) was not an established government and could not be considered a coherent alliance of Augment-led nations, either. Instead, it was a conglomeration of nations, corporations, institutes, military forces (national, rebel and mercenary) and individuals that -in theory- were seeking to shape the future of Earth in the way that could be considered pro-Augment, but instead worked against that greater goal almost as much as it worked for it.
The progeny of the failed Chrysalis Project found themselves spread throughout the world upon the projects collapse, growing up in their native cultures but largely finding success through the advantages with which they were bred. The greatest of these, Khan Noonian Singh, attempted to inculcate a sense of collaboration between these corporate, military and world leaders, but often found himself the target of his own 'siblings', as many attempted to become the leader of the Augments, or even the planet.
There were plenty of huge successes attributed to this Great Khanate (a misnomer that implies cohesion), such as with space technology, but the political unrest that came with the competition between the Augments and the governments actively seeking to reign them in, led to great suffering and loss of life.
Agencies
As the Great Khanate was never a coherent entity, there are no 'official' agencies ascribed to it. However, it did achieve its recorded successes via the efforts of organizations associated with it, including countries, corporations and military units.