In the fandom world, people tend to get their knickers in a bunch when the writers don't listen to rules and circumstance layed down in past episodes, and no showrunner has more canon to contradict than Doctor Who's Steven Moffat. Fans tend to have a love-hate relationship with him, due to the fact that he tends to kill off characters we like--a lot--but will he be the one to kill the Doctor himself?
While I have no way of knowing for sure, I suspect that the answer is NO! For one thing, it is rumoured that Moffat will be leaving the show after this coming season. But the question of just how many times a Time Lord can regenerate isn't voided if the show is taken over by someone else. Let's take a closer look at regeneration.
The idea of regeneration was introduced when William Hartnell's health started to interfere with his ability to play the Doctor. The show was doing well, but it's star wanted to quit. Then-showrunners John Wiles and Donald Tosh attempted to help Hartnell off the show, but were blocked by head of serials Gerald Savory, who vetoed numerous other changes. Wiles and Tosh quit, and their replacements--Gerry David and Innes Lloyd--found themselves with far more freedom at the hands of Savory's replacement, Shaun Sutton. And so the two set to work finding a way to work in a new lead actor.
At this point, it hadn't yet been established for sure that the Doctor wasn't human, and script editor Davis proposed that the Doctor's species had the ability to die and then return in a new body. Producer Lloyd built upon this by adding that the Doctor could undergo this "renewal" process regularly, transforming from an older man into a younger one. And here's a fun fact: the physiological process of regeneration is based on the psychotropic effects of LSD. Since then, it had been stated, and, surprisingly adhered to that regeneration is possible because of the TARDIS, though the reasoning behind this has varied over the years. In some cases, it is because the TARDIS itself has restorative properties, while in others it is a combination of this and Time Lord biology. More recently, in "A Good Man Goes to War."it was determined that conception on board the TARDIS can give the resulting child Time Lord DNA, which is why River Song can regenerate.
However, that's not to say the entire thing has always been set in stone: Lloyd and Davis intended for the initial "renewal" to merely be the Doctor making himself younger, and the Second Doctor's forced transformation into the Third suggested a complete cosmetic overhaul wasn't a normal part of things. It wasn't until Pertwee's regeneration in Planet of the Spiders that regeneration as we know it was solidified, and it's been suggested by many a pedant that Hartnell, Troughton, and Pertwee are all the same Doctor as a result of this.
The first time that a limit on regeneration is mentioned is a full ten years after the first regeneration happened on the show. In The Deadly Assassin, it is stated that a Time Lord has twelve regenerations, meaning thirteen incarnations in all. When that was set forward in 1976, I can't imagine that anyone could have predicted that this "fact" would make it out of the serial, as writer Robert Holmes (and indeed most Who writers) had no problems contradicting their earlier work if it made a better story. Hell, the Deadly Assassin itself dismantled a claim made by The Brain of Morbius, earlier that same year, also by Robert Holmes, that Tom Baker was the Twelfth Doctor.
It was in the 1980s, with John Nathan-Turner's turn as producer, that Who grew a head for continuity, and for some reason it picked up on the "thirteen lives" tidbit. It started out innocuously enough--after all, that limit was what had resulted in the killing off of the Master, and restoring him required addressing it. (The problem was solved by making the Master a bodysnatcher.) But references to the supposed limit continued, often simply as minutia for minutia's sake (the 80s were quite fond of this), until "thirteen bodies total" ascended to the ranks of "Time Lord" and "from Gallifrey" as one of the absolute immutables of the Doctor's life, cemented in the public consciousness for better or for worse. (Russel T Davies attempted to fix this with The Sarah Jane Adventures serial, Death of the Doctor, by having the Eleventh Doctor state that he has 507 lives. The fandom, predictably, revolted, and Davies decided to claim he had been joking.)
There are two things that would allow for the Doctor to have extra lives. Firstly, in "Let's Kill Hitler", the Doctor was dying and River Song healed him by using her extra regeneration energy, thus using up the rest of her lives on him. We know that she was in her third body at the time, so that may have given the Doctor a whopping ten more regenerations. It is, though, also true that the Doctor used some regeneration energy to heal River's broken wrist in "The Angels Take Manhattan", but I do not expect that it was all of his remaining lives, as he now has great control over the use of the energy as exhibited in part two of The End of Time, as he is able to hold off regenerating until he has gotten his reward.
The other way that the Doctor may be able to regenerate more than twelve times is the idea that the twelve life limit was a rule of Time Lord society and not a law of their biology. This concept has been hinted at several times over the years--most people like to point out the Time Lord High Council offering the Master a completely new regenerative cycle in The Five Doctors, and an FAQ the BBC released regarding Series 4 seems to back this up.
Also, we must consider that despite our wildest dreams that these tales of the Doctor and his TARDIS are based in fact, when it comes down to it, Doctor Who is a business, and a wildly lucrative one at that. Anyone with a brain knows that making money is a good thing and as long as the show doesn't go into the red, it will likely keep going.
So when it comes down to the meat of it, I doubt that the twelve-life rule will stop the show. If it does, I'll eat my fez.
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