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)

Civil War
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. At the end of his experiments, the Second Doctor implanted the Human Factor into a group of Daleks who became friendly to the Doctor and whom the Time Lord named Alpha, Beta and Omega. When these Daleks travelled back to Skaro, the Doctor, pretending to be infected with the Dalek Factor which in reality did not affect Time Lords, tricked the Emperor into believing he would implant the Dalek Factor into these Daleks and eliminate the threat. Instead, the Doctor rigged an archway in the Dalek City, causing it to instil the Human Factor in every Dalek that passed through it. Those Daleks who passed through the archway began to question orders from their superiors. When the Emperor's guards attacked, the Humanised Daleks retaliated. They turned on the Emperor and the Dalek Civil War broke out.

The fighting spread to the throne room amid the Emperor's protests and declarations. The Emperor himself was probably destroyed, although a blinking light on his casing may have indicated his survival. The Dalek City was devastated by the conflict and began to explode. The Doctor believed this battle to be "the final end." The civil war also brought the Great War to an end. (TV: The Evil of the Daleks, PROSE: The Evil of the Daleks)

Aftermath
Nevertheless, the Doctor was ultimately proved wrong as the Daleks survived, with the Emperor's forces defeating the humanised rebels. (COMIC: Bringer of Darkness) Some of the humanised Daleks managed to escape destruction and 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) The victorious imperial forces began rebuilding. 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, which also referred to the Last Great Time War as the "Great Time War", so the book's accuracy is questionable (though "Great Time War" was later used by Engines of War).
 * 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 [sic].

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 2005-2010 design.