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So my best reconstruction of the climax of the Heresy in the Warhammer 40,000 universe (which, it must be said, is a production of Games Workshop) is that the Emperor, who was flesh and blood yet godlike in stature and power, had created many sons to execute his benevolent dictatorship over the worlds of mankind; yet roughly half of them, led by his favored son, had rebelled against him in favor of unfettered power.

And so it was that the favored son, the leader of the rebellion, had fought his way into the Emperor's throne room, and was engaged in mortal combat with his father, the two of them being roughly matched; perhaps the son was slightly stronger. One of the Emperor's loyal sons, seeing his father gravely wounded yet continuing to fight, was consumed with battle-fury and tore apart several of the rebellious leader's bodyguard with his hands before his elder brother killed him with a mere thought.

That distraction was enough for the Emperor to strike, and banish his eldest son's soul from his body. But by that time he had been wounded beyond healing. He consented to have his body placed in a permanent life-support system, and as he rested within it his mind was free to wander, yet his body was still inert and nearly lifeless. He was said, by his loyal followers, to have "ascended to the Golden Throne."

While he had lived and moved about freely, he had told his subjects time and again that he was not a god, he was merely their king; he had told them that salvation for humanity was not to be found through superstition and worship of gods nor through construction of ever more advanced technology, for these had led to aeons of strife and a machine rebellion, but rather humanity would have to save itself through responsibility and care for all its members. (He was not an atheist; the gods were manifestly real, but made poor leaders.) But after his fall - or his ascension, as his followers said - he was again worshipped as a god, and countless atrocities were perpetrated in his name.

The Emperor, imprisoned for ages now in his useless body, nonetheless speaks mind-to-mind with certain of his subjects, imparting to them his true will or useful lessons. They may be honored and respected as prophets, but it is more likely for them to be burned as witches. It is believed that he also speaks in the same way with his bodyguard, an elite cadre of superhuman soldiers, but they are too secretive for this to be a safe conclusion. Mostly, though, those who hear his voice hear him crying.