(MAJOR SPOILERS for Across The Darkened City by David Bartlett, the second story in Doctor Who: The Companion Chronicles: The First Doctor volume 2 and I do mean MAJOR, this is basically all about the big reveal of the story).
Doctor Who canon is really weird. On the one hand you have a series that has a profound love affair with its own past which produces sequels all the time. I'm posting this between the transmission of two episodes featuring a version of the Cybermen not used on television since 1966 for really no better reason than as a thank you to a lead actor who loves the design. On the other hand, there are few people who can claim Doctor Who canon has any consistency.
According to televised Doctor Who, not bringing in any later expanded universe material, the Doctor both built from scratch and stole the TARDIS; the Brigadier retired from UNIT half a decade before meeting Sarah Jane Smith at UNIT; the same author wrote the story that established the Doctor has only thirteen lives, co-wrote one that established that Tom Baker was the Twelfth Doctor and then wrote Davison's (therefore Thirteenth) Doctor's regeneration.
When you start subbing in EU material it only gets stranger: Peri has three or four different fates (two of them even produced by the same author for the same company); Ace has at least five; Sarah Jane dies in 1997, a decade before her own TV show begins where she is neither a corpse nor a zombie; Gallifrey is destroyed twice; the Eighth Doctor leads several contradictory lives.
So sometimes you just have to shrug and pick the explanation you prefer. You don't have to choose. I've nothing against The Sarah Jane Adventures but I also loved Bullet Time, the novel that kills off Sarah Jane. Sometimes, though, you end up with a clash where you pick a side almost on reflex.
Across The Darkened City is a two-hander in which Steven and a semi-functional Dalek are the only survivors of a spaceship crash. There's an abandoned Dalek transmat on the other side of a ruined, monster-infested city and if Steven drags the Dalek there on a cart the Dalek will chip off back to Skaro and give Stephen the co-ordinates for the planet he was abducted from (and where the TARDIS currently is). Its a pretty standard such shipwreck story where the Dalek elicits some sympathy and the two start working together in a way that suggests both are suffering some element of Stockholm Syndrome. Its a decent story and Nick Briggs does his usual excellent job with the Dalek vocals.
An element that comes up every now and again is that the Dalek is a special, superior form of Dalek that “needs” to survive and return to Skaro. Across the story its suggested that this Dalek has empathy and is preserving Steven's life for more reasons than sheer pragmatism.
The bit I like about the twist I'm about to describe is that the way this Dalek acts, with a degree of emotional intelligence enough to manipulate Steven into not just helping it but sympathising with it, is an interesting way to link the Hartnell era Daleks with the Troughton era version. This Dalek has been engineered to display the emotional intelligence the Daleks display in David Whitaker's two Dalek stories which makes it superior to the Daleks as imagined by Terry Nation (it helps that I am absolutely on the side of Whitaker in this particular debate).
Then it turns out this isn't just some random genetically re-engineered Dalek because in the final scene it gets put in a new casing, gets a deeper voice and turns out to be the Emperor.
Now, as unfashionable as it is to disbelieve that John Peel (not the sainted DJ) contributed anything of worth to the Dalek mythos, one idea I always loved (from his Evil of the Daleks novelisation) was that the Emperor was the very first Dalek, the one who shot Davros in Genesis. It made a beautiful sense to me that in a society of total conformity with no names and barely any form of rank (nothing seems to exist between mission commanders and drones) the only true distinction that could nominate an ultimate authority figure was killing the creator of your entire species.
He's the Emperor because he killed “god” and in my own personal headcanon I'm sticking with that. It just seems a bit more fitting than having the Emperor being another random Dalek experiment.
That's just my humble, of course. Its Doctor Who canon, do as thou wilt is the whole of the law.