The destruction of Skaro by the Hand of Omega led to the closing phase of the Dalek Civil War. With Davros' power base destroyed and Davros himself stranded in an escape pod at an unknown location in space and time, the Loyalist Daleks routed the remaining Imperial Daleks and exterminated them.
A new Emperor was gestated from stored genetic material of the old Emperor and given access to all Dalek records. This new Emperor realised that in order for the Daleks to survive, they needed to be focussed and willing to learn from past mistakes. This change in philosophy enabled the Daleks to spread out once more, complex and devious plans were developed that would further the goals of the Dalek race and lead them towards their goal of universal domination. This marked the beginning of a new Generation for the Daleks.
Having destroyed Davros' initial uprising and with Skaro uninhabitable, a number of old Dalek bases were reactivated and the power base was spread across these so as to minimise the possibility of a single strike destroying the entire Dalek leadership. The Emperor designed an improved version of its Emperor casing and made the process that transferred him to the smaller "Prime" casing even more efficient.
As its new base of operations, a mobile location was chosen – a virtually impregnable Dalek Kill-Cruiser much larger than the norm. From here, the Empire could be monitored and the Emperor could travel where required. An early priority was the location of Davros. Reports arrived of a Dalek fleet leaving the vicinity of Earth’s Solar System. The Emperor mounted a task force which caught these "human" Daleks unawares and totally destroyed them. Davros' fate is unsure; however it is unlikely the Emperor would waste a scientific resource of this calibre.
Before launching spearheads for invasion, the Emperor made sure sufficient forces were available to wipe out any opposition. No longer assured of their own infallibility, the Emperor instigated a programme of research which resulted in augmentations for itself and other Dalek mutants, together with enhancing the Mark Three Travel Machines that protected the majority of their forces. Research into Time Travel began in earnest once more. This generation came to an end following a second invasion of Earth's galaxy. It seemed to most that the Daleks just vanished. In truth, they were preparing for their next offensive – this time against allifrey and the Time Lords.