During the course of invasion into Mutters Spiral, a new Emperor was gestated by the Dalek Supreme that had temporarily assumed control of the Empire and instigated the invasion. The new Emperor's first action was to review the last few thousand years of history. Analysis of this history led the Emperor to decide that in order to become the supreme power in the cosmos, one race above all others must be destroyed.
The seeds of the Last Great Time War had been planted before the Daleks were even created and several skirmishes had already taken place between the two races, including an aborted attempt to exterminate the Time Lord High Council using duplicants of the Ka Faraq Gatri and his companions and the Apocalypse Element incident, which resulted in the re-creation of the Seriphia Galaxy. Time Lord agents had repeatedly been involved in thwarting Dalek plans over the course of the millennia, the Time Lords had even gone so far as to try and avert the creation of the Dalek race.
This fact proved to the Emperor that the so called Lords of Time considered them a true threat. All Dalek units were recalled to the Seriphia galaxy and an intensive research programme began to refine the Daleks own Time technology. This included not only technologies that helped make travel through time easier, but also weapons and defences that may be required during a war with a race that had mastery of time for millions of years.
Under the direction of the Emperor Dalek, a new outer casing was designed. Bulkier, more heavily armoured and with advanced manoeuvrability, the Mark Five Casing was designed to withstand even the technology of the Time Lords. These casings featured the pinnacle of Dalek engineering, allowing complete autonomous flight, vast amounts of fire power and unparalleled defensive measures.
This generation was almost entirely wiped out during the Time War. There were a few survivors of the War – some Dalek drones were thrown through the vortex and the Cult of Skaro escaped with a captured Time Lord Prison Ship into the Void between universes, for example.
The Cult of Skaro re-emerged into the universe during the early twenty-first century in the city of London on planet Earth. Here they attempted to release the prisoners from the captured ship in order to re-vitalise the Dalek Empire. During the course of this event, they came into conflict with not only the forces of Earth, but also The Doctor and primitive Cybermen from another universe. Ultimately, the Ka Faraq Gatri managed to defeat the Cult – sending all the Daleks back into the Void. The Cult of Skaro managed to escapte by instigating an emergency temporal shunt that nudged them out of danger.