On the day before the end of the Time War, the War Doctor went to Skaro and destroyed most of the Emperor's fleet. (PROSE: The Day of the Doctor [+]Steven Moffat, adapted from The Day of the Doctor (Steven Moffat), Target novelisations (Target Books, 2018).)
The Emperor's ship itself later survived the "inferno" which ended the War. Emerging in the post-Time War universe, the Emperor led a new fleet and army of Daleks, amounting to 200 Dalek saucers and about half a million Daleks, in an invasion of Earth in the year 200,100, only for the fleet to be wiped out by the Bad Wolf. (TV: Bad Wolf [+]Russell T Davies, Doctor Who series 1 (BBC One, 2005)., The Parting of the Ways [+]Russell T Davies, Doctor Who series 1 (BBC One, 2005).)