Originally the natural psychic forces of all animals and plants flowed harmoniously which created a unifying force flowing through all living beings. As intelligent races developed, their extremely potent minds filled the warp with very powerful energies, which were not harmonious. These negative energies, in time coalesced in to troublesome spots, which then grew in size, developing a consciousness of their own resulting in the chaos powers.
The new man
The primitive man, the hunters and harvesters of ancient times had a special relationship with the warp. The natural energies of the warp flowed harmoniously through them too. Some humans were more sensitive to these energies, and being able to discern subtle variations, were able to predict future occurrences and therefore benefit their communities. These were the witch doctors; the shamans; the psychics. However as humans and their civilisations developed, their myriad feelings such as power ambition and greed began to disturb the natural flow of the warp. This inevitably made the warp less accessible to the shamans and also detached the human race from their natural connection to the warp. These new forces became localised forming new focuses in the warp resulting in the formation of the chaos powers.
Birth of the Emperor
When shamans, those humans with the gift of tapping in to the warp died, their souls entered the warp bathing and flowing with the natural energies until reborn in another body. However, with the disturbances in the natural rhythm of the warp that humanity created, this was becoming more difficult. Souls were bring lost to the malign predatory chaos powers that now emerged in the warp. As their ability to lead and protect their communities receded, the worried shamans began a long debate and research lasting hundreds of years. At its conclusion they realised that they were doomed , as they would gradually be consumed by the warp entities, and that without them, all of mankind was doomed to the predations of the chaos powers. They finally concluded that the only hope for mankind was to pool all their energies in to he creation a single immortal being, who would guide humankind to heir destiny. Being immortal, he would not need to be reincarnated and thus not be t the mercy of the chaos powers in the warp. Shamans in their thousands committed suicide and their kind was gone forever from the earth. Their energies coalesced together in the warp and within an year was born as a single entity of immense power. The new man. The emperor of mankind!
The Emperor's early years on earth
For thirty eight thousand years the immortal New man wandered the earth, first observing but then taking on various personae to guide and advance humanity. But as the human race prospered the warp became disturbed by their myriad thoughts and emotions and its natural flow could no longer sustain the planet. Despite the New mans' best efforts, the intrinsic traits of martial honour, self satisfaction and ambition resulted in persecution and war. These emotions also fed the newly developing powers in the warp.
The Emperor and the Chaos powers
Even before the coalesced emotions and psychic forces in the warp developed their own consciousness, they sensed the presence of the new man and that this Emperor was their greatest enemy. Khorne, the blood god, was the first of these chaos powers to fully awaken, as massive wars swept throughout the earth. This was followed by Tzeentch, the Changer of ways as nations developed political intrigue and diplomatic manipulations. Finally Nurgle, the god of plague awoke, sweeping the earth with famine and disease. By the middle ages, all three had fully awaken.