Doctor Who: EXACTLY Where Jo Martin's Doctor Fits Into Doctor Who Canon
All of which brings us back again to another version of the original question; where does this new Doctor fit into the regeneration cycles?
There are a couple of options from the modern show, such as Tennant's rejuvenation and hand-growth regeneration not counting, but I believe the answer has to do with those other faces that were shown during the psychic battle in The Brain Of Morbius. The implication was strong that these were past faces of the Doctor, as other versions of him that we did know were also shown. Could it be that Hartnell was the First Doctor but not the first incarnation of the man? That would mean that Troughton was not his second form, but one of several that had come before.
It would also mean that it's likely a whole new regeneration cycle was started between Troughton's end and Pertwee stumbling out of the TARDIS. A regeneration cycle that had entirely been wiped from the Doctor's mind, with the gaps tied together to make him think he'd only lived a few lives up until then.
But why would the Time Lords remove so much information from the Doctor's mind, returning him to the exile they promised him anyway? Why would he run away from the job he's been given, exiling himself in a way, and be chased by a homicidal Time Lord? Could it be that the Doctor, famous for sticking his nose in where it doesn't belong, had found out something the Time Lords had been hiding from even themselves?
“They lied to us. The founding fathers of Gallifrey. Everything we were told was a lie. We’re not who we think, you or I. The whole existence of our species... built on the lie of the Timeless Child.”
And what is the Timeless Child? A story for another time and, perhaps, another season.