Board Thread:The Panopticon/@comment-6032121-20190914173756/@comment-6032121-20200910133706

The Doctor hoping Davros died at the Shoreditch Incident seems like one of the things that make more sense if you assume that the Doctor was mistaken in Nemesis of the Daleks, that the Nemesis Emperor was in fact the Dalek Prime unbeknownst to him, and that he realised his mistake off-screen. But that's all rather speculative. The Doctor lies, time is rewritten, yadayada — hell, the Doctor might even be using a metaphorical sense of "dying", treating Davros's apparent degeneration into an amnesiac Emperor as seen in Nemesis of the Dales as the Kaled scientist having functionally died. I think we're good with saying it's Davros in Nemesis, but the Dalek Prime in Emperor!.

As concerns the Emperor in Defender of the Daleks, he is pretty explicitly the Golden Emperor, or at the very least an Emperor from before the Time War: upon meeting him, the Tenth Doctor explicitly goes "The Emperor of the Daleks!" (emphasis mine) and complains that of all the individuals a time paradox could resurrect, it had to be this guy. (Though that's not strictly part of the narrative, the "character profile" on the first page of the comic book also identifies the Emperor as a returning enemy who has squared off with the Doctor before.) With him looking the way he does, I think it's beyond any reasonable doubt the Golden Emperor/Dalek Prime.

The story is not set during the Last Great Time War — it is set in the "present" of the Tenth Doctor era, but in temporally-anomalous circumstances whose nature has yet to be elaborated upon. The Doctor identifies the existence of the Prime's entire Empire (which includes a reconstructed Dalek City identical to the one in Series 9) as "a paradox", and the Daleks, to his surprise and confusion, don't remember ever having fought in a Time War against the Time Lords, instead believing themselves to have been at war with the Hond for ages.