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The Dalek Emperor was the supreme ruler of the Dalek Empire, commanding the Dalek race and the planet Skaro.
History
Dalek Prime
One of the first Daleks, who exterminated Davros and proclaimed the Daleks' future victory over the universe (TV: Genesis of the Daleks), assumed the role of Dalek Prime (later Dalek Emperor) and would continue to act as the Emperor throughout Dalek history. (PROSE: War of the Daleks)
The Golden Emperor
After the neutronic war that devastated Skaro, the mutants had survived in the casings. The only humanoid Dalek survivors of the war, Yarvelling and the warlord Zolfian encountered a Dalek which persuaded them to build more Dalek casings for their mutated descendants. Before the last two humanoid Daleks died, a special casing was built for the Emperor to reflect its new rank, made of Flidor gold, quartz and Arkellis flower sap. The Golden Emperor[1] was slightly shorter than the other Daleks, with a disproportionately large spheroid head section rendered in gold rather than grey. It also had three globes on each panel unlike other Daleks. (COMIC: Genesis of Evil)
The Emperor within the Dalek City
The next known incarnation of the Emperor remained in an enormous, immobile, conical shell plugged into a corner of the control room in the Dalek City on Skaro. It was connected to the wall by tubes, and spoke in an echoing voice.
This Emperor tried to win the wars by blackmailing the Second Doctor. He 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. He was seemingly destroyed by a civil war between humanised Daleks and un-altered Daleks. However, a light was seen blinking on its casing at the end, indicating some kind of activity. (TV: The Evil of the Daleks, PROSE: The Evil of the Daleks)
The Emperor survived when his forces began rebuilding, resulting in the emergence of a new command structure involving grey Dalek drones and Gold Supreme Daleks (TV: Day of the Daleks)
Shortly after this, the Emperor met Bernice Summerfield, who the Emperor questioned on why the Civil War had occurred. (AUDIO: The Lights of Skaro)
Davros as Emperor
Davros was made the Emperor of the Imperial Dalek faction of the Daleks during the Imperial-Renegade Dalek Civil War. He was encased in a customised Dalek casing with a dome top which could open and close, his body below his head and shoulders covered in a mass of tubing and cables, implying he had greatly deteriorated physically. He was last seen heading for an escape pod just before his ship was destroyed in the wake of the supernova (set off by the Hand of Omega) that consumed Skaro. (TV: Remembrance of the Daleks) Later, Davros' increasingly unstable mind was obliterated by a totally Dalek personality, that of the Emperor. This new Emperor took command of Davros' Daleks and departed. (AUDIO: Terror Firma)
By the time the Tenth Doctor met Davros after the Last Great Time War, Davros' old personality had regained control. (TV: The Stolen Earth)
Emperor of the Dalek Empire
When the Daleks launched an invasion of the Milky Way from the Seriphia Galaxy, the Dalek Emperor was in command. While it successfully conquered much of the galaxy, its real goal was Project Infinity. It intended to summon Daleks from another reality. When those Daleks turned out to be appalled by genocide, the Emperor was captured by the Earth Alliance (AUDIO: "Death to the Daleks!", Project Infinity) but transmitted its consciousness into a human, Susan Mendes, to continue the war. (AUDIO: Dalek War: Chapter One) It erased her consciousness and intended to use her form to con the galaxy into lowering its guard; however, a psychic trap caused the remnants of Mendes to awaken and trigger the destruction of all Dalek technology, removing the Emperor from it's human host. (AUDIO: Dalek War: Chapter Four)
During the Time War
The Emperor in its original form resided in Kaalann on Skaro. When Skaro was devastated, he was thought to have been killed. (GAME: City of the Daleks) But the Emperor had survived and later formed the Cult of Skaro, a group above and beyond the Emperor himself, to "think as the enemy thinks" and "imagine" new ways to find victory (TV: Doomsday) and during the Time War, he terrified the Master by taking control of something significant called "the Cruciform". (TV: The Sound of Drums) The Emperor oversaw the creation of the Eternity Circle, and was present when they created the Temporal Cannon to use against the Time Lords. (PROSE: Engines of War)
The Dalek Emperor was aboard its saucer flagship when all the incarnations of the Doctor up to the Twelfth moved Gallifrey to a pocket universe on the last day of the Time War, the assembled Dalek fleet ended up firing on itself through the space Gallifrey once occupied (an event which was presumed to have been the activation of the Moment) (TV: The Day of the Doctor); as such, the Emperor was believed to have died with the rest of its species, but this was mistaken. (TV: The Parting of the Ways)
Surviving the Time War
The Emperor's lone ship barely survived the Time War, falling through time in a heavily damaged state. The nine-meter tall Emperor's new casing had the appearance of its mutant revealed floating in a transparent tank of liquid, topped by a giant-sized Dalek dome, complete with eyestalk, flanked by panels of armour dotted by Dalek "bumps" with a ring-shaped "throne" on the bottom. It went into seclusion at the edge of the Solar system "damaged but rebuilding" during the Fourth Great and Bountiful Human Empire. Circa 199,909, it secretly installed the Jagrafess aboard Satellite Five to play the "long game" of slowly manipulating humans and re-establishing the Dalek species and fleet. A hundred years after the Jagrafess was killed, in the year 200,100, the Emperor was still using Satellite Five (now renamed the "Game Station") to manipulate humanity and conceal his fleet. (TV: Bad Wolf) The Emperor secretly used transmat technology aboard the space station to kidnap humans for nearly two hundred years. The kidnapped humans were harvested for their genetic material, and "one cell in a billion" was used to rebuild a new race of Daleks (TV: The Parting of the Ways) numbering roughly half a million aboard a fleet of 200 ships. (TV: Bad Wolf) Because the Emperor had recreated the Dalek race, it saw itself as a god and immortal and so was worshipped by the new Daleks. These and other religious concepts such as blasphemy were new to Dalek psychology. (TV: The Parting of the Ways)
The Emperor's pawn aboard Satellite Five, the Controller, hated her masters and transmatted the Ninth Doctor aboard the Game Station to help defeat them. (TV: Bad Wolf) When he encountered the Emperor and his new religiously fanatical Daleks, the Doctor surmised that they were driven insane both because they isolated themselves for so long, but also because they were in denial of the fact that they were part human. The Daleks killed almost everyone aboard Satellite Five, and they attacked Earth, bombing millions of people, to transform it into the Emperor's "temple". Shortly afterwards, the Doctor turned down his chance to use an uncalibrated delta wave to destroy all nearby life, human and Dalek alike. The Emperor thought he was victorious, but he and his entire fleet were atomised by Rose Tyler after she had absorbed the energies of the time vortex and became the Bad Wolf temporal paradox. (TV: The Parting of the Ways)
The Progenitor Dalek Emperor
When the New Dalek Paradigm went back to the ruined Skaro, they created a new Emperor Dalek, reusing the shell of the old one, albeit with new paint. His blue colouring suggests he was a Strategist Dalek, had ties to that role or was the mastermind of all of the Daleks' plans for universal conquest. When the Eleventh Doctor and Amy Pond travelled back in time to when Skaro was devastated and before the new Daleks arrived with the Eye of Time, they erased the Daleks' alterations and Kaalann was left abandoned. The new Emperor was never created as a result. (GAME: City of the Daleks)
When the New Dalek Paradigm took control of Earth in 2106, they were led by a new Emperor Dalek. This Emperor was different from the Time War Emperor, as it was coloured purple, was able to form a sphere and its weaponry was much larger. This new Emperor wanted to completely change time by using a piece of the Eternity Clock, and remove Gallifrey from existence; the Daleks would then become the new Lords of Time. The Eleventh Doctor and River Song were able to remove the piece of the Eternity Clock from the Dalek's possession, foiling the Emperor's plans and undoing the Dalek invasion of Earth. (GAME: The Eternity Clock)
The Daleks later established a Parliament, and were led by a Prime Minister instead of an Emperor. (TV: Asylum of the Daleks) Though whether this Prime Minister is a full-time leader or exists to resolve internal disputes is as yet unknown.
Other references
A Dalek Emperor from an alternate timeline placed its mind into a Thal and travelled back in time to warn the Daleks of a great catastrophe that would devastate their race. He realised he had caused the alternate timeline and prevented it, thus erasing himself from existence. (AUDIO: The Mutant Phase)
A Dalek Emperor composed the plan to send the Master to divide the humans and Draconians, and gave him a squad of Ogrons to complete his task. (AUDIO: The Dalek Conquests)
Personality
As the supreme ruler of the Daleks, the Emperor showed a very bossy attitude, barking orders with confidence, and had perhaps the most individual personality of his species. Like all Daleks, he was very racist towards other species and believed in the superiority of his race above all else, using very degrading and infuriating terms when discussing how it had recreated the Dalek race following the Time War's end. This act brought about the most profound change in his mindset and personality, as it caused the Emperor to think of himself as an immortal god, with his "bretheren"(creations) worshiping him as such. Because of this, he arrogantly believed he couldn't be hurt, which led to his demise. The Emperor was very deluded about its Dalek race, claiming it had "cultivated pure and blessed Dalek", and called Rose Tyler's statement that they were half human blasphemy, when in fact he himself was the only pure Dalek present. Unique among Daleks, the Emperor was one of the few Daleks to display a sense of humor, as he playfully chided the Ninth Doctor when the latter was threatening to use a Delta Wave to destroy him, saying he'd enjoy to see the Doctor become just like him, "The Great Exterminator". Having dealt with him in the past and witnessed his capabilities, the Emperor notably did not underestimate the Doctor's intellect and acknowledged the fact that his old enemy had nearly destroyed the Dalek race at the end of the Time War. (TV: The Parting of the Ways)
On an alternate timeline a Dalek Emperor in Ganatus's body listened to the Fifth Doctor not to change the past and he and the Mutant Phase were erased from existence. (AUDIO: The Mutant Phase)
During the invasion of Mutter's Spiral. The Dalek Emperor had interest on Susan Mendes and the Project Infinity. He told the Supreme Dalek that they were the only ones with access of the Kar-Charrat information and would kill her only on his command. (AUDIO: Invasion of the Daleks, The Human Factor, Project Infinity)
When the New Dalek Paradigm rebuilt Kaalann and altered time with the Eye of Time, a blue Dalek Emperor recognised the Eleventh Doctor and declared the Daleks will be the masters of time and the universe. He told the Doctor that he won't take orders and asked the Doctor to fear the Eye of Time. The Dalek Emperor told him and Amy that the Daleks were the new Time Lords and ordered the Daleks to stop them when they jumps to the Eye. (GAME: City of the Daleks)
Behind the scenes
According to the non-narrative material Doctor Who: The Dalek Handbook, the Emperor in the Dalek City survived the Great Civil War and would revamp the Dalek command structure, as well as focus his strategies on rewriting the Dalek timeline.
The Dalek Emperor is a minor villain in LEGO Dimensions.