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The Emperor never made the mistake of underestimating the threat of Chaos, and in order to meet that threat he put the best scientific brains on Earth to work. Weapons and spacecraft poured out of the Martian factories to bolster beleaguered forces throughout the galaxy.
The Emperor's most long-sighted plan to counter the insidious influences of the Chaos Powers was the creation of the Primarchs: genetically engineered super-humans with god-like powers. The Emperor's intention was to create a whole race of super-humans from the genetic blueprint of the Primarchs. By making them loyal and strong he hoped that they would prove immune to the malign psychic influences of Chaos.
The Primarchs were to be shining examples of humans free from the taint of corruption. The energy of the uncorrupted warp would flow through them as it flowed through the Emperor himself, invigorating them and conferring special powers such as were possessed by the shamans of old.
Unfortunately, things did not go quite according to plan. Despite the Emperor's best attempts to shield the project from the penetrating eyes of the Chaos Powers they still managed to learn of it. The Primarchs were still in their foetal stage, growing in special amniotic tanks, when the Chaos Powers combined their energies to spirit them away in an unexpectedly bold move.
Even for the Chaos Powers this kidnapping represented a colossal expenditure of energy. The Primarchs were sucked through the warp and scattered on separate human worlds in distant parts of the galaxy. The Chaos Powers did not have the resources to destroy the Primarchs, but they did the next best thing which was to hide them from the Emperor. They were to remain hidden until after the waking of Slaanesh.
The Emperor had lost the Primarchs and the first action of his renewed war against the Chaos Powers. The Primarchs could not be recreated and even if this were possible there was not time to do it. The birth pangs of Slaanesh grew louder and louder as the time of his waking grew near. The Emperor evolved another plan. Using genetic material which had been imprinted from the Primarchs into laboratory gholems, some of their qualities could be reproduced as discrete biological organs. By implanting these organs into a young growing body a person with some of the qualities of the Primarchs could be created. In this way the first Space Marines Chapters were founded. Each Chapter utilised genetic material derived from one of the Primarchs.
By the time that the warp storms were ended, the Space Marines and other Imperial forces were ready to begin their reconquest of the galaxy. The forces of Chaos were already strong, and many human worlds had been taken over by Chaos Cultists or other aliens. It was a long hard struggle, but with every victory the Imperium grew stronger as new warriors joined the Great Crusade.
The initial conquests concentrated in areas where the Primarchs had been hidden. Using his psychic powers the Emperor gradually located and found each of his original creations and united them with the Space Marine Chapters created from their genetic imprints. They seemed none the worse for their brush with Chaos, having grown up to be great leaders and warriors among the local human populations. In fact this appearance of normality was to prove deceptive, for some of the Primarchs had become tainted by their early contact with Chaos. With the help of the Primarchs the Great Crusade swept across the galaxy. Humanity rose to the task of rebuilding its ancient heritage, and everywhere the alien oppressor was defeated and driven out. Chaos retreated to its own realms, to the zones of warp-real space overlap such as the Eye of Terror.
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