During the Last Great Time War, a Dalek Emperor resided in Kaalann on Skaro. (GAME: City of the Daleks) He formed the Cult of Skaro, a group above and beyond the Emperor himself, created to "think as the enemy thinks" and "imagine" new ways to find victory. (TV: Doomsday) The Emperor took control of the Cruciform. (TV: The Sound of Drums, AUDIO: The Heavenly Paradigm) Towards the end of the War, the Emperor oversaw the creation of the Eternity Circle, and was present when they created the Temporal Cannon to use against the Time Lords. The Emperor witnessed the other temporal weapons used against human prisoners, like the former governor to Moldox, Jocelyn Harris who had betrayed her people to work for the Daleks as their puppet. The Emperor watched as Jocelyn was removed from history as a demonstration. (PROSE: Engines of War) When Skaro was devastated, the Emperor was thought to have been killed. (GAME: City of the Daleks)
The Dalek Emperor was aboard its saucer flagship when all thirteen incarnations of the Doctor moved Gallifrey to a pocket universe on the last day of the Time War. The assembled Dalek Fleet ended up firing on itself through the space Gallifrey once occupied, an event which was presumed to have been the activation of the Moment; (TV: The Day of the Doctor) as such, the Emperor was believed to have died with the rest of its species, but this was mistaken. (TV: The Parting of the Ways)
The Emperor's lone ship barely survived the Time War, falling through time in a heavily damaged state. The nine-metre tall Emperor's new casing had the appearance of its Kaled mutant revealed floating in a transparent tank of liquid, topped by a giant-sized Dalek dome, complete with eyestalk, flanked by panels of armour dotted by Dalek "bumps" with a ring-shaped "throne" on the bottom. It went into seclusion at the edge of the solar system "damaged but rebuilding" during the Fourth Great and Bountiful Human Empire while it used any humans that stumbled upon it to create a new army of Daleks, and it steadily rebuilt it's fleet.
Circa 199,909, it secretly installed the Jagrafess aboard Satellite Five to play the "long game" of slowly manipulating humans and re-establishing the Dalek species and fleet. A hundred years after the Jagrafess was killed, in the year 200,100, the Emperor was still using Satellite Five, now renamed the "Game Station" to manipulate humanity and conceal a Dalek fleet. (TV: Bad Wolf) The Emperor secretly used transmat technology aboard the space station to kidnap humans for nearly two hundred years. The kidnapped humans were harvested for their genetic material, and "one cell in a billion" was used to rebuild a new race of Daleks (TV: The Parting of the Ways) numbering roughly half a million aboard a fleet of 200 ships in just a century. (TV: Bad Wolf)
Because the Emperor had recreated the Dalek race, it saw itself as a god and immortal and so was worshipped by the new Daleks. These and other religious concepts such as blasphemy were new to Dalek psychology. The Emperor had become insane due to the fact it had been in hiding for so many centuries. (TV: The Parting of the Ways)
The Emperor's pawn aboard Satellite Five, the Controller, hated her masters and transmatted the Ninth Doctor aboard the Game Station to help defeat them. (TV: Bad Wolf) When he encountered the Emperor and his new religiously fanatical Daleks, the Doctor surmised that they were driven insane both because they had isolated themselves for so long, but also because they were in denial of the fact that they were part human. The Daleks killed almost everyone aboard Satellite Five, and they attacked Earth, bombing millions of people, to transform it into the Emperor's "temple". Shortly afterwards, the Doctor turned down his chance to use an uncalibrated delta wave to destroy all nearby life, human and Dalek alike. The Emperor thought he was victorious, but he and his entire fleet were atomised by Rose Tyler after she had absorbed the energies of the time vortex and became the Bad Wolf temporal paradox. (TV: The Parting of the Ways)
Rose would later gloat over her destruction of the Emperor which she revealed in her confrontation with Dalek Sec, enraging him to the point that he was only stopped short of exterminating her by the arrival of the Tenth Doctor. (TV: Doomsday)