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Has the limit on regenerations for Time Lords shown in The Time of the Doctor always been canon, or was this was made up just for this episode?

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The question is a reasonable one but it is also worth noting that the idea of "canon" does not have the same "weight" in Doctor Who as it does in, say, Star Trek. See tardis.wikia.com/wiki/Tardis:Canon_policy for some interesting discussion. –  Eric Lippert Dec 27 '13 at 6:08
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The regeneration limit is old canon from the Tom Baker era as established in "The Deadly Assassin". It comes up a number of times thereafter. Particularly in the context of the Valeyard from the Colin Baker era and various schemes of the Master to "get more lives" as it were.

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it just occured to me, tho: in "The Angels Take Manhattan" Eleven used some of his regeneration energy to heal River, but if he was out of regenerations, where did that come from? –  Michael Edenfield Dec 27 '13 at 2:48
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The consensus on that seems to be that he had some reserves of regen energy but not enough to transform. It's possible that it was left over from when she blew all of her regens on him. –  World Engineer Dec 27 '13 at 2:50
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The canon limit is from the Fourth Doctor (Tom Baker) in The Deadly Assassin and was recently changed / modified In The Time of the Doctor.

"The Time Lords gifted the Doctor a new cycle of regenerations. He then proceeded to control the regenerative energy gifted to him and shoot down the Daleks with it, destroying many ships in huge blasts of energy. This however may only be used after receiving a new cycle of regenerations."

See also:

Why were there 13 Doctors prior to #12?

RE: The Deadly Assassin:

This is the first story to reference the fact that Time Lords get 12 regenerations and 13 lives. Recent interviews with the production team behind the 2005-present revival (including David Tennant in Doctor Who Magazine #415) have made it appear as if the allocation of 13 lives in this story is a piece of minutia unique to this story. In fact, the 13-life limit has been a major plot element of at least three other stories, both of which involve villains attempting to steal the Doctor's remaining regenerations: TV: The Keeper of Traken, TV: Mawdryn Undead and the 1996 TV movie. All of these stories reference the 13th life limit in dialogue. Several other Time Lords have been encountered since The Deadly Assassin in later stories who have reached their 13th and final incarnation, namely Azmael and Salyavin.

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One reason I dislike Wikipedia: The last sentence of that quote is just made up; in particular, River Song used her regeneration energy as a weapon after only her 2nd regeneration, so it does not appear to have anything to do with a new regeneration cycle. –  Michael Edenfield Dec 27 '13 at 2:03
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As written, it clearly claims that The Doctor only has control over his regeneration energy "after receiving a new cycle of regenerations.", which I claim is simply not true. –  Michael Edenfield Dec 27 '13 at 2:29
    
No. It does not say that. He has control over THE NEW CYCLE because he had already used up all his other regenerations. "This however may only be used after receiving a new cycle of regenerations." It makes sense that he can only do this after receiving a new cycle. He was OUT of regenerations. The gift allowed him to fight. It is not only when you get new regenerations, but when you have some to spare. –  Meat Trademark Dec 27 '13 at 2:39
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If that's what that paragraph is trying to say, than it needs to be seriously re-written, because that's not at all what it actually says. "This may only be used" means something very different from "The Doctor could only use this" –  Michael Edenfield Dec 27 '13 at 2:48
    
@MeatTrademark: I think you’re misunderstanding what Michael Edenfield is saying. He understands the last sentence is related to the preceding paragraph. That’s the problem with it. It says that the events described in the preceding paragraph (i.e. the Doctor using regeneration energy as a weapon) could only happen because the Doctor had just received a new cycle of regenerations. That’s a problem because there wasn’t anything in the episode (that I noticed) to suggest that rule, and it doesn’t fit very well with some previous regenerations (which have, for example, damaged the TARDIS). –  Paul D. Waite Dec 27 '13 at 12:35
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