Doctor Who season 12 revealed the Doctor is secretly the Timeless Child, and it's possible she had her true memories all along. Doctor Who showrunner Chris Chibnall can hardly be faulted on his ambition; in season 12 he upended decades of continuity, revealing the Doctor is not a Time Lord at all. Rather, she is the Timeless Child, a being who potentially predated the universe itself and who became the base genetic code for the entire Time Lord race.
It's the biggest change in Doctor Who lore since the Time Lords were introduced all the way back in 1969. According to the Timeless Child retcon, William Hartnell was not the First Doctor at all; rather, there were a billion years of past Doctors, stretching all the way back to the founding of the Time Lord race. The Time Lords erased all memory of these past incarnations when they forcibly regenerated the Timeless Child back to a young boy, and the Doctor grew up never knowing his true origin.
No doubt the Doctor Who Holiday Special and season 13 will continue to build on the Timeless Child retcon, which raises all sorts of intriguing questions: if the Doctor is not a Time Lord, what is she? What happened to the pre-Hartnell incarnations, and why did the Time Lords erase all knowledge of the Timeless Child? And what exactly happened to the Timeless Child memories?
The Time Lords Have The Power To Extract Memories
The Time Lords have long been known to have the power to extract memories. In the classic series, "The Five Doctors" saw the Time Lords intend to subject a Castellan - whom they believed to be a rogue - to a device called the Mind Probe. Nothing was revealed about the process, but the Castellan's reaction strongly suggested it is an agonizing process, and in fact he apparently chose to commit suicide by attempting to flee rather than face the Mind Probe.
The David Tennant era took this idea one step further, revealing the Time Lords have the technology to both extract memories and implant false ones. The two-part story "Human Nature" and "The Family of Blood" saw the Doctor choose to hide himself on Earth by using a device called the Chameleon Arch. This technology rewrites a Time Lord's genetic code, allowing them to live as a member of another race; it extracts the Time Lord's memories and replaces them with a constructed identity. The memories are then stored within a device that can be opened to unlock the Time Lord's true memories and reverse the process. In the Doctor's case - and, later, in the Master's - the device was a fob watch with a perception filter placed upon it to ensure it wasn't opened by accident. It's important to note this process was apparently an incomplete one, though, because the Doctor's human identity - John Smith - still found himself haunted by dreams of gods and monsters, Time Lords and Daleks. A trace aspect of the memories was still there, meaning the extraction process was imperfect.
Did The Time Lords Use The Chameleon Arch On The Doctor?
All this raises the intriguing possibility that the Time Lords used the Chameleon Arch when they erased the Doctor's pre-Hartnell memories and forcibly regenerated her/him into a child. That would fit with a strange subplot in the episode "Ascension of the Cybermen," featuring a mystery man named Brendan. His story was apparently a Matrix-created parable of the Timeless Child; he was found as a baby by two adoring adoptive parents, integrated into the local community, and took a job as a police officer. In a shocking twist, he survived what should have been a fatal incident, and then was subjected to an agonizing experiment. According to the Master, this final shot represented the erasing of the Timeless Child memories, and it looks markedly similar to the pain Tennant's Doctor endured when he was subjected to the Chameleon Arch.
Because the Chameleon Arch wasn't 100 percent effective, leaving trace memories that occasionally bubbled to the surface, this fits well with the classic series of Doctor Who, where there are numerous clues that can now be said to point towards the Timeless Child retcon. The First and Second Doctors both claimed to have invented the TARDIS, rather than stolen it outright; Tom Baker's Fourth Doctor seemed far too comfortable with the idea of entering other universes in the story "Planet of Evil"; and Sylvester McCoy's Seventh Doctor clearly believed he was far more than "just a Time Lord." The Tom Baker episode "The Brain of Morbius" actually showed what were intended to be pre-Hartnell Doctors, but they were forgotten as a continuity error, until Chris Chibnall brought them back as incarnations of the Timeless Child.
All this matches up surprisingly well, meaning it's entirely possible the Timeless Child's memories were stolen from the Doctor by the Chameleon Arch; they left traces, which occasionally rise to the surface, and some Doctors sensed more of their true past than others. But if the Time Lords did indeed use the Chameleon Arch, it raises the question of just where the Timeless Child memories are concealed.
The Doctor's Fob Watch May Hold The Timeless Child Memories
The Doctor has always been a great collector, treasuring mementos of his past; in his very first story, "The Power of the Daleks," Patrick Troughton's Second Doctor reminded viewers of that fact when he ferreted through a trunk. One of these beloved possessions could indeed be the crucial device containing the Timeless Child memories, hidden behind a perception filter so the Doctor never looks at it too closely. The most likely object is another fob watch because several Doctors have worn what seemed to be the same fob watch as part of their costume, and it has rarely been used for anything other than hypnotic suggestion. It's true Paul McGann popped open his fob watch in the 1996 Doctor Who TV movie, but this had a different design than the one seen in the costumes of William Hartnell, Patrick Troughton, Tom Baker, Colin Baker, and Sylvester McCoy.
Showrunner Chris Chibnall is an old-school Doctor Who fan, which explains why the Timeless Child retcon fits better with the classic series than the relaunch. The Timeless Child draws upon countless small hints and clues in Doctor Who's established lore, and it would certainly be Chibnall's style to reveal the truth about the Timeless Child had been part of the series right from the start. If this is the case, then at some point in the future - either in the Holiday Special or in Doctor Who season 13 - Jodie Whittaker's Thirteenth Doctor will pop open her fob watch and learn the secrets the Time Lords had hidden from her all this time.