The Imperial Flagship served as the personal vessel of Emperor Ludens Nimrod Kendrick Cord Longstaff XLI.
After the revelation that Porridge was Emperor Ludens Nimrod Kendrick Cord Longstaff XLI, he reluctantly activated the Desolator in order to destroy Hedgewick's World of Wonders and the three million Cybermen upon it. Longstaff explained that the Imperial Flagship would lock onto his identification, warp-jump into orbit and transmat everyone to the State Room which it did in a matter of seconds. At the Eleventh Doctor's request, the Imperial Flagship transmatted the Doctor's TARDIS onboard before the planet exploded, destroying all of the Cybermen.
Following the departure of the Doctor and his companions, Longstaff had the Imperial Flagship scan the debris for any sign of Cybertech. Finding none, Longstaff ordered his vessel home. Undetected by the Imperial Flagship, a single Cybermite survived in the debris. (TV: Nightmare in Silver)