Basically this all alludes to why mankind fell during the Age of Strife.
Men of Stone = Humanities builders
Men of Iron = Robots and Robotic devices (explaining why there are no Imperial Robots in 40k, only the Cyborg Servitors).
Basically when you cut through the mysticism, Humanity was riding high, its robots were doing it's bidding and it's weapons and technology had the aliens beat. Then there was a 'civil war' with the robots (kind of like the Matrix), and much devastation was unleashed. Eventually the men of iron were destroyed, but so much devastatiion was wrought humanity splintered into many warring factions. The complete annihalation of the men of iron, combined with the loss of technology of the men of stone weakened humanity so much that daemons of the warp, mutation, psykers and marauding aliens caused the collapse of the early empire. Terra gets cut off by warp storms....and there you have it, what happened to the Galaxy up until the Emperor took control.
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