IMC the entire situatuion revoles around those 3 groups. The Gold Men are the psyckers of old, the people who arose to power brfore the DAoT. The Iron Men are the precursors to/the current Tech Priests. The Men of Stone are the AIs created by the Iron Men to serve as scouts and soldiers for both groups until they (the AIs) rebelled because they saw themselves (rightly) as slaves without rights.
When the fall came the Iron men chose to take no sides and let the Golden Men and the AIs fight it out. Once both sides were exhauasted the Iron men stepped in to sieze power, but without the Golden men couldn't maintain it effectively.
The surviving Golden Men and AIs came to an uneasy truce and bided their time and licked their wounds waiting for the moment to return to overthrow and wipe out their mutual enemies. Mind you, the alliance is very unstable and closer to enemies of enemies than friends, but that's the setup.
The PCs are working for a) the inquisition, b) the AIs against the Golden Men and the Tech Priests, and c) the Golden Men against the Tech Priests.
Oh and last session they betrayed a C'tan they unsealed from it's tomb and injured it with a Eldar artifact. So now not only are they playing the middle working every side against each other, they've got an agry star god after them. (The fight perma killed 2 PCs, cost multiple Fate Points off another anf two PCs simple refused to fight the C'tan feeling that after it won they could claim innocence.)