The Dalek flagship was the main warship of the Dalek Fleet. Like many of the other ships, it was a flying saucer, but was many times larger than the size of the standard Dalek flying saucer.
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The Exterminator was a flagship, the first of its kind and was placed under the command of Dalek X, the Dalek Inquisitor General, during the Second Dalek War. The ship was considered by the Daleks as the ultimate expression of power, and contained 510 Daleks. The Doctor, in his tenth incarnation, helped destroy it on Hurala. The Exterminator's destruction was a stunning loss to the Dalek Empire and it gave Earth what was needed to be able to push the Dalek fleet out of Earth-Space. (PROSE: Prisoner of the Daleks)
During the Dalek invasion of Mutter's Spiral, the Imperial Command Ship was the flagship of the Dalek fleet and travelled to Lopra Minor for Project Infinity. (AUDIO: Project Infinity)
On the last day of the Last Great Time War, the flagship fell through time (TV: The Parting of the Ways) and the Void (PROSE: The Whoniverse) and arrived around the 2000th century. The ship housed the Dalek Emperor, which was wired directly into the ship and slowly repaired it after it was heavily-damaged, and the Emperor's Personal Guards. The flagship held one hundred thousand Daleks.
When the Fleet invaded Earth in 200,100, the flagship had missiles to fire at targets and hangars from which Daleks could be launched. The ship, as well as the Fleet and every Dalek, was destroyed when Rose Tyler became the Bad Wolf entity. She proceeded to divide them at the atomic level until nothing remained but dust. (TV: The Parting of the Ways)
During the New Dalek Paradigm's invasion of Earth in 2106 using a piece of the Eternity Clock, the Dalek Emperor oversaw the proceedings from a Dalek Flagship, one which the Eleventh Doctor claimed he had never seen the likes of before. This flagship contained hundreds of thousands of Daleks. (GAME: The Eternity Clock)