The Secret of the Emperor was a comic story original to The Dalek Outer Space Book, a Dalek annual of the 1960s. It revealed that the early Dalek Empire had actually been a nominal democracy, depicting the Dalek Prime's overthrowing thereof in favour of ruling unquestioned as a permanent Dalek Emperor.
This story also culminated in the Emperor moving from a small, mobile casing to a huge one with an augmented brain, located in a hall in the Dalek City. Although the design of it was different, it was indeed in a similar situation, rather than as the mobile figure of earlier Dalek comics, that the Emperor appeared the next year in The Evil of the Daleks.
This report shows all Dalek Commanders, due to this being Super-Skaro year, returning to Skaro from "distant galaxies" on the occasion of the yearly re-election of the Golden Dalek as Dalek Emperor and of his loyal aide the Black Dalek as the Empire's Warlord. The Black Dalek acts as master of ceremonies, and states as an obvious fact that the current Emperor will once more be reelected because all Daleks know him to be "the greatest brain in the Universe".
However, for the first time ever, dissent arises. The Commander of the Red Extra-Galactic Squadron explains that in their travels through many galaxies, he and his Daleks have discovered that humans keep outwitting Dalek strategies, proving that a change of leadership is needed. The Black Dalek begins to reply, only for the outraged Emperor to cut him off and order the entire Red Squadron's immediate destruction.
However, after the deed is done, the Emperor begins to doubt himself, wondering "if it is possible that [he is] not perfect", after all. After locking himself in his private quarters for weeks pondering this question, the Emperor reemerges having concluded that he is indeed imperfect. He has a group of Scientist Daleks take his casing apart with the mission of improving his mechanically-augmented brain, while the Brain Machine, into which the Emperor has poured all his knowledge, temporarily handles the government of Skaro.
While they are taking the Emperor apart, the Scientists decide to examine the Emperor's memory cells concerning Dalek-Earthman conflicts, to try and figure out for themselves how the Daleks have fallen behind. Instead, they discover how the Emperor began to malfunction: while headed back in time to 2415 as part of an attempted invasion of Earth, the Emperor's personal time machine malfunctioned and sent him back to the Battle of Agincourt, where, lost and bewildered, he was "charged and bowled over" by knights who thought him to be "a midget in golden armour".
The Emperor was able to adjust his time machine and dematerialise again, but never at the correct date, his memory cells having been damaged by the knights; "again and again, he tried", only to find himself in increasingly hostile time periods, such as a prehistoric Earth where he faced a gigantic sea reptile and had rocks thrown at him by cavemen. Meanwhile, the Daleks who had arrived in 2415, bereft of their leader, had to surrender.
The Scientists also discover that the Emperor's sonic guard was cracked, presumably during the invasion of Uranus due to Earth using supersonic waves against the Dalek Galactic Ships. Finally, the Emperor's new casing, including an organic but artificial "main brain" to supplement his organic one, is assembled in the Great Hall. The investigator attaches a schematic of the new casing, alongside a dire warning to Earth, all of its scientists and all of its space commanders, concerning the renewed Dalek threat that this represents.
- Golden Emperor
- Black Dalek Leader
- Commander of the Red E.G. Squadron
- Chief Scientist
- The Dalek Emperor's new artificial brain produces radiation that threatens even the "jelly-like" mutant itself, necessitating its container being isolated.
- The Chief Scientist wears a protective Dalekoat to work on the Emperor's casing.
- The last page of the comic doubled as one of the annual's "feature," a full-page schematic of the Dalek Emperor's casing's internal workings.
- The Black Dalek once again enforces the Golden Emperor's supremacy with deadly force in the face of dissidence. (COMIC: Duel of the Daleks)
- The Second Doctor would later meet the Emperor residing in a large, static casing in the Dalek City, designed to boost the mutant's intelligence. (TV: The Evil of the Daleks, PROSE: The Evil of the Daleks)