Dalek Civil War The Dalek Civil War was a civil war fought on Skaro between the Dalek s loyal to the Dalek Emperor and the humanised Dalek s , who had been implanted with the Human Factor . History . 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 " ) 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 brough the Great War to an end . ( TV : " The Evil of the Daleks " , PROSE : " The Evil of the Daleks " ) 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 Dalek s . ( TV : " Day of the Daleks " ) Behind the scenes . " The Dalek Handbook " . According to the 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 Dalek s replaced Black Dalek s as Supreme Dalek s . 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 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 .