During the Last Great Time War, the flagship fell through time in the final stages 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)
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 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 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. (GAME: The Eternity Clock)