Dalek Civil War

The Dalek Civil War was a civil war fought on Skaro between the Daleks loyal to the Dalek Emperor and the humanised Daleks, who had been implanted with the Human Factor by the Second Doctor.

Origins
The origins of the Dalek Civil War could be traced back as far as the year 4000, over one thousand years before it took place, with the Daleks' attempted invasion of the solar system via use of the Time Destructor. (TV: The Daleks' Master Plan) The failure of the invasion alerted several galactic powers, Earth among them, to the threat of the Daleks and numerous war forces were assemble to go to war against the Dalek Empire over the course of the following millennium, sparking the Great War which threatened to destroy the Daleks. (PROSE: The Evil of the Daleks)

Human Factor experiment
In a last-ditch effort to prevent this, the Dalek Emperor tasked the Supreme Council the responsibility of capturing the Doctor so he could be blackmailed into discovering the secrets of the Human Factor. From that, the Daleks could discover the Dalek Factor which they could spread throughout human history and prevent the Great War from ever happening. (PROSE: The Evil of the Daleks)

Making contact with Theodore Maxtible, a scientist in 1866 researching time travel, the Daleks promised to give him the secret of alchemy in return for his aid. To gain the obedience of his colleague, Edward Waterfield, Maxtible helped them take his daughter, Victoria hostage. On the Daleks' instructions, in 1966 Edward arranged the theft of the the Doctor's TARDIS from Gatwick Airport and subsequently lured the Second Doctor and Jamie McCrimmon to the Daleks' time machine, using it to take them back to 1866.

Using Jamie as an unwilling subject by studying him whilst he attempted to rescue Victoria, the Doctor was able to isolate the Human Factor. He subsequently implanted it into a group of Daleks who became friendly to the Doctor and whom he named Alpha, Beta and Omega. In identifying the Human Factor, the Doctor had inadvertently enabled the Daleks to identify the Dalek Factor. With the experiment successful, all the Daleks returned to Skaro and Maxtible was ordered to bring Waterfield, the Doctor and his friends too. (TV: The Evil of the Daleks)

The rebellion
The three Humanised Daleks returned to their duties on Skaro. At the same time an archway to implant Dalek Factor was tested successfully on Maxtible and subsequently utilised on the Doctor. Unknown to the Daleks the arch had no effect on the Doctor as he was not human, however he pretended it had in order to sabotage the arch so it would implant the Human Factor instead.

After his guards began to report incidents of the Humanised Daleks beginning to question orders, the Doctor suggested the Emperor have all Daleks pass through the conversion archway to quell the unrest. The Emperor accepted his suggestion, unaware every Dalek that passed through the archway had the Human Factor instilled instead. Those Daleks who passed through the archway began to question orders from their superiors, prompting violent retaliations from the Emperor's guards. The Humanised Daleks defended themselves, urged on by the Doctor who encourged them to seek explanations from their Emperor personally. As the Doctor rallied them, one of the Emperor's guard attempted to kill him. Edward Waterfield pushed him out of the way, taking the blast himself. As he died, the Doctor promised to look after his daughter and then fled the City whilst the Humanised Daleks pushed on into the throne room.

The fighting spread to the throne room amid the Emperor's protests, as his guards defended him from an onslaught of Humanised Daleks. The Emperor himself sustained significant damage, although a blinking light on his casing may have indicated his survival. The Dalek City was devastated by the conflict and began to explode. Observing the destruction from nearby cliffs, the Doctor believed this battle to be the Daleks' "the final end." (TV: The Evil of the Daleks)

The Doctor was ultimately proved wrong as the Emperor's forces defeated the rebels, (COMIC: Bringer of Darkness) with the surviving Humanised Daleks forced to flee Skaro. (COMIC: Children of the Revolution) The civil war brought the Great War to an end. (PROSE: The Evil of the Daleks)

Aftermath
The Time Lords believed that the civil war resulted in a resulted in a temporary absence of Daleks from Skaro. (PROSE: Dalek Combat Training Manual) The surviving humanised Daleks found a new home on the planet Kyrol. Alpha was one of them and acted as their leader. They would ultimately destroy themselves to prevent the telepathic parasite Kata-Phobus from feeding on them. (COMIC: Children of the Revolution)

Though the Emperor was thought destroyed in the civil war, the Time Lords acknowledged the possibility that, given the Daleks' extraordinarily long lifespan, the organic part was retrieved. (PROSE: Dalek Combat Training Manual) Indeed, the victorious imperial forces began rebuilding. At some point, Jamie McCrimmon and Victoria Waterfield returned to the Dalek City themselves; sneaking into the silent, darkened throne room, they were shocked to find that they had walked into the lion's dun, with the Emperor alive and well and more Daleks than ever standing guard above him, who triumphantly declared that "the Daleks [had] returned". (HOMEVID: Emperor of the Daleks) In his third incarnation, the Doctor first encountered a new Dalek command structure, involving grey Dalek drones in place of silver ones and Gold Dalek commanders as superiors to Black Daleks. (TV: Day of the Daleks)

Behind the scenes

 * The name "Great Civil War" was used to refer to the conflict in the reference book Doctor Who: Aliens and Enemies.
 * In the video game City of the Daleks, the Eleventh Doctor tells Amy that the last time he visited Kaalann, it was in ruins and the Daleks had fled, suggesting the civil war took place on Kaalann, although he may also have been talking about the Time War. The Dalek Handbook also states that the Dalek City was named Kalaann.
 * Dalek: The Astounding Untold History of the Greatest Enemies of the Universe later affirmed that Kalaann and the Dalek City are the same location, though PROSE: The Day of the Doctor would establish that the Doctor visited the Dalek City during the Last Great Time War, establishing the Eleventh Dioctor is not talking about the civil war in City of the Daleks.

The Dalek Handbook
According to the non-narrative material the reference book The Dalek Handbook, the Dalek Emperor survived, the humanised Daleks were defeated by the Emperor's Daleks, and the race began to rebuild. As evident from Day of the Daleks and Frontier in Space, a new command structure was put in place: grey Daleks replaced silver Daleks as drones and Gold Daleks replaced Black Daleks as Supreme Daleks. For a time, Ogron mercenaries were hired to compensate for the huge number of Daleks lost in the conflict.

Doctor Who: Battles in Time
According to non-narrative information in DWBIT 35, the war was fought around the same time as the defeat of the Seventh Dalek Armada at the battle of Gurnian. An account of the conflict was taken by a Dokktor Whit-Arkker in his document entitled "The End of the Daleks". These Daleks were depicted in the magazine as being of the modern bronze design.