Dalek Prime

Originally known as either the Dalek Prime or Genetic Variant Two-One-Zero, this Dalek Emperor ruled the planet Skaro and the Dalek Empire, and was the first Emperor of the Daleks the Doctor encountered.

The Doctor was well aware of the Emperor and he wondered if they would ever meet.

This Emperor was an enormous, immobile, conical shell installed into a corner of the control room in the Dalek City, connected to the wall by tubes and cables, and spoke in an echoing voice. Unlike the rest of its race, it had no gunstick.

Becoming the Emperor
According to one account, the Emperor used to be “Genetic Variant Two-One-Zero”, one of several genetically-modified Daleks sent to pass an ordeal. On the planet Shade, it had to collaborate with Steven Taylor to survive Chaons who infested the planet and to get to a transmat station to escape. Several times Steven saved Two-One-Zero from death, once taking it out of its casing and carrying it in his hands wrapped in a tarpaulin. During the whole ordeal, Two-One-Zero exhibited qualities unusual for Daleks: he tried to save human prisoners' lives and exterminated another Dalek to save Steven's life. He promised to give Steven a transmat code to return back to the First Doctor and Vicki on the planet Entropica, but betrayed Steven in the very end, giving him transmat coordinates that would lead him to certain death had he not been saved by the First Doctor. Upon returning to Skaro, Two-One-Zero demonstrated that it was indeed a superior Dalek as it was the only genetic variant to return from the ordeal. It was transferred to a new casing and declared itself the Emperor of Daleks, its experience with Steven prompting it to search for the Human Factor as a way to achieve total Dalek domination over the universe. (AUDIO: Across the Darkened City)

Another similar albeit different account stated that the Emperor was originally the Dalek Prime, the Dalek that exterminated Davros. (TV: Genesis of the Daleks) Following the end of the Thousand Year War, the Dalek Prime began conducting experiments on other life-forms on Skaro, creating mutations which went on to inhabit the petrified jungle and the Lake of Mutations near the foot of the Drammankin Mountains. Eventually the Dalek Prime discovered the molecules that could cause further mutation within a Dalek, and created a drug from its research which would initiate the mutation. Not prepared to test the drug on any Dalek in case it grew beyond its capabilities, the Dalek Prime used the drug on itself and evolved to the peak of Dalek evolution with hugely enhanced mental powers. Afterwards, it proclaimed itself the Emperor of the Dalek race. (PROSE: The Evil of the Daleks)

Search for the Human Factor
After accepting that the Daleks were losing the Great War after centuries of denial, the Emperor tried to win the conflict by blackmailing the Second Doctor. It ordered the Daleks to capture the Doctor so that they could force him to conduct research into the Human Factor. This would unlock the secrets of the Dalek Factor which was to be spread throughout all areas of human history, giving all humans the mentality of a Dalek and preventing the Great War from ever happening. When the Doctor escaped, the Emperor was caught in the chaos of a civil war between humanised Daleks and un-altered Daleks and nearly destroyed. However, a light was seen blinking inside its casing at the end, indicating some kind of activity. (TV: The Evil of the Daleks, PROSE: The Evil of the Daleks)

Shortly after this, the Emperor met Bernice Summerfield as she moved through time, and questioned her on why the Civil War had occurred and why the other Daleks questioned him. She berated the Emperor during their short discussion, mocking it for not even having a gun, and walked away so that she would live, giving "the greatest insult [she] could think to give a Dalek". The Emperor was left screaming after her for her to obey him and that she would be annihilated. (AUDIO: The Lights of Skaro)

Having survived, the Emperor's forces began rebuilding, (COMIC: Bringer of Darkness) resulting in the emergence of a new command structure involving grey Dalek drones and Gold Supreme Daleks. (TV: Day of the Daleks)

Creating/Erasing the Mutant Phase
In an alternate timeline where the Daleks came under attack by the infection called the Mutant Phase, the Dalek Emperor still commanded the empire from Skaro, the Fifth Doctor commenting that they'd both "had a face-lift" since they last met. As the Mutant Phase swarm destroyed Skaro, the Emperor was able to place its mind into the body of the Thal Ganatus, possessing him, and ordering the Doctor to take him back to the 22nd century Dalek invasion of Earth, where the Mutant Phase started. Travelling back in time, the Emperor tried to warn the Daleks of the great catastrophe that would devastate their race, but the Doctor explained that his interference is what caused the mutation in the first place. When the Emperor realised this, he chose not to change the past, erasing both himself and the Mutant Phase from existence. (AUDIO: The Mutant Phase)

Behind the scenes

 * This Emperor is the first Dalek Emperor in the television series proper.
 * In the non-narrative book The Dalek Handbook, it is said that the Emperor actually survived the Great Civil War despite his apparent demise in The Evil of the Daleks, subsequently refocusing his strategies on time manipulation. This suggests that he and any number of chronologically-later Emperors are actually one and the same.
 * In the novelisation of The Evil of the Daleks, the Dalek Prime becomes this Emperor. Although this seems to be contradicted by Across the Darkened City, there are similarities in circumstances. Both the Dalek Prime and Two-One-Zero are genetically-advanced Daleks who declared themselves Emperor.