The Emperor was never meant to stay on the Throne, he had planned to use it to aid in healing his injuries. He is an Eternal, one of a handful of beings who cannot die, a trait which he passed to his son Vulkan (who is still roaming the galaxy).

After he was placed there it was realised by certain factions that his "sacrifice" could be used to better control humanity, and the 'God-Emperor' concept was truly born. However, other factions nknew the truth, and attempted to free the Emperor. This led to a schism that is still felt 10,000 years later in the Inquisition.



The Throne is now beginning to fail thanks to 10,000 years of continued use, and the Tech-Priests do not know how to fix it. When it stops the Emperor will rise, signalling the return of the Primarch's. The Lion is slumbering within the Rock, Vulkan is wandering the galaxy, Guilliman is in stasis (his wounds healing despite this), Russ promised he would return (the 13th Company will precede him, and they've returned), and Dorn is out there (remember only a forearm was found, not a whole body). And don't forget Corax (who is the master of stealth) and the Khan (the Warp always gives back what it takes).