Doctor Who season 12 has introduced a new version of the Doctor and made some major changes to the timeline, seemingly creating a TARDIS plot hole in the process. Jodie Whittaker's sophomore season as the Time Lord has seen showrunner Chris Chibnall take some big swings with the established canon of Doctor Who: there's a new Master, played by Sacha Dhawan; a new mystery to solve in the shape of the Timeless Child; and now, a new incarnation of the Doctor, hiding on Earth as a woman called Ruth Clayton (Jo Martin).
While the first two were big, the latest is the most shocking reveal of all. There was an unknown version of the Doctor hiding on Earth as a human (thanks to a Chameleon Arch), complete with her own weapon (a gun rather than a sonic screwdriver), and her own ship, which is of course a TARDIS designed to look like an old police phone box. That may be a common part of Doctor Who lore and thus not too surprising to see a Doctor with their iconic ship, but it raises some big questions about where Ruth fits within the timeline and how that relates to the First Doctor. Whittaker's Thirteenth Doctor has no memory of ever being in the form of Ruth; likewise, Ruth has no recollection of ever being Whittaker. What's more, Gallifrey still exists in Ruth's timeline, but not Whittaker's, likely ruling out her being from Thirteen's future (and if that were the case, then why not simply wait to get there in a future season and a regeneration?).
This suggests that Ruth's Doctor is actually a forgotten version who came before William Hartnell, making her the real First Doctor. This could help explain why Thirteen has no memory of her, but also just why Ruth has a TARDIS that's interior looks extremely similar to the one used by the First Doctor (a design that has changed over the years with subsequent regenerations). There's one problem with that, however: the TARDIS only looks like a police box because the Chameleon Circuit broke when Hartnell's Doctor came to London in 1963, settling on the design that's since become so famous. So if Ruth is before Hartnell, why is the TARDIS already a police phone box?
There's no easy answer to that mystery. One possible explanation might be that Ruth is from a later point in the timeline - there's a gap between Patrick Troughton's Second Doctor and Jon Pertwee's Third that could potentially work - but Ruth having no knowledge whatsoever of the sonic screwdriver suggests that isn't the case (the sonic was introduced with the Second Doctor). Doctor Who has a long history of retconning itself and showing that what we thought happened wasn't actually the case. Indeed, that's a defining part of season 12 in particular, which has already changed Gallifrey's fate, brought a new Master in, and positioned a mystery that changes the very existence of the Doctor, the Master, and the rest of the Time Lords. It's not impossible, then, that the established history of Hartnell's Doctor and his TARDIS isn't actually the truth of what happened. It's true we've seen Clara with the First Doctor, but again, little of the past can be assumed to be correct now given the big changes at Time Lord history that are suggested in Doctor Who season 12.
The exact specifics, however, of how the TARDIS could have existed as a police box before the First Doctor, and for him to be convinced of its different origin, is another matter entirely, but perhaps something Chibnall has in store for the future of Doctor Who. After all, if there's a mystery hidden deep within the memories of the Doctor and the Master, then it's possible this TARDIS was changed too, and could even factor into it. The Time Lords re-writing history isn't much of a stretch, after all.