As the Horus Heresy raged across the stars, the Emperor was still at Terra. During this time, he sent his closest friend Melcador the Sigilite to combat the rebellion, while he was unable. It took the Emperor a long time to be convinced that Horus, his favorite son has betrayed him. Even then he did not want to fully accept it.
Melcador, on the other hand, was fully aware of what happened and what was happening in the galaxy. He set several plans in motion. He started sending assassins to kill various traitor Primarchs. Most of them were targeting Horus and all of them failed to accomplish their goal. He started laying the groundwork for a new organization that will have ultimate power in the entire Imperium of Man, with no restrictions, the Inquisition. Only after the Horus Heresy will they be able to come to full power. The last of the major plans Melcador set in motion was the creation of the new type of Space Marines, the Grey Knights. Made specifically to fight demons. More powerful, better equipped and all powerful psykers.
After years of war, Horus and his traitors managed to reach Terra itself. This was made possible by having half of the Mechanicum join him. Horus was in a tight situation. He was losing the siege of Terra and he had an entire almost untouched legion coming close to the Sol system, the Ultramarines. Two hundred and fifty thousand Space Marines., this was not a fight he could win. To give himself a chance he lowered the void shields on his flagship. This allowed the Emperor and two of the Primarch to teleport. They were scattered and had to find their way themselves to find Horus.
The Emperor could have simply killed Horus the moment his void shields were down, but he wanted one last chance to see for himself what happened to his favorite son. After Horus killed one of his brother, Sanguinius, the Emperor confronted him. They fought hurting each other, but the Emperor was holding back the whole time. It took the death of a lone Guardsmen to make the Emperor finally give his all and kill Horus.
After the battle, the Emperor was badly hurt and was dying quickly. Just before his death, he was placed on the Golden Throne. An ancient device that kept him alive for all eternity. As long as the device was operational. He was not fully alive, nor was he dead, but in a state in between.
In the 41st Millennium, the Emperor is regarded as a god of humankind. He guides the ships by powering the Astronomicon. He can sometimes perform miracles and even bring faithful back to life.
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