Driven insane by the fall through time and the long period of rebuilding in the "Dark Space", the Time War's Emperor began to see the world through a new eye. In creating a new race of Daleks, it found parallels with figures discussed in the Earth's media – gods. The Emperor began to think of itself as the God of Daleks and its survival of the Time War seemed to point towards its own invulnerability, infallibility and a divine purpose. The Emperor began to think of the hated Ka Faraq Gatri as being the equivalent of the devils who oppose God. It looked forward to a final meeting with the Time Lord – for the Emperor was sure he would survive to be encountered once more.
In purely physical terms, the Emperor was identical to its appearance during the Time War. Located in the heart of the gigantic flagship, the Emperor remained unscathed by the ravages of the escape through the Vortex with minimal protection. The Emperor's mental state was another matter however. The loss of everything and the effects of the vortex finally pushed the creature over the edge. As plans were hatched to ensure the survival of the Human race, the Emperor became aware of the concept of "gods" through the Earth media. In its insanity, it came to the realisation that it was itself a god – and therefore invulnerable to harm. Earth would become an "Eden" for the new race of Daleks.
Maintaining only a number of Elite Guards to defend the throne room of the Flagship, the Emperor demolished the old hierarchy, ensuring all Daleks were subordinate and loyal to itself only. Initially, this abolition was necessary due to the low numbers of Dalek units surviving the Time War however, as time progressed the Emperor grew more and more delusional and assured of its omnipotence.
