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The Dalek Flagship was the main warship of the Dalek Fleet. Like many of the other ships, it was a flying saucer, but many times the size of the standard Dalek flying saucer.
During the Last Great Time War, the flagship fell through time and arrived during the 100,000s. The ship housed the Dalek Emperor, which was wired directly into the ship, 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. (DW: The Parting of the Ways)
There were other Dalek flagships in Dalek history before the Time War. Another flagship, by the name of the Exterminator, was 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. The Doctor in his tenth incarnation helped to destroy the flagship. The Exterminator's destruction was a massive loss to the Dalek Empire and it gave Earth what was needed to be able to push the Dalek fleet right back out of Earth-Space. (NSA: Prisoner of the Daleks)