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In The Stolen Earth we witness The Doctor get fatally wounded by a Dalek's blast while reuniting with some of his companions.

They bring him into the TARDIS where he starts to regenerate. However, after he has healed himself, he fires his regenerative energy into his severed hand to prevent changing his appearence.

Now, it has been said that Time Lords only have 12 regenerations (13 lives, currently the doctor is on his 11th, looking back this episode states that limit)

Would this act of using the regenerative energy but not transforming count towards his 12 limit?

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I don't think this question has an answer until the show's writers decide to give it one. They control the universe; it will count if they say it does. –  FredH May 4 '13 at 0:05
    
You could also argue that the current Doctor is in his 12th regeneration if you subscribe to the theory of the 'missing' Doctor between the McGann and Eccleston incarnations. –  Nobby May 8 '13 at 21:39

2 Answers 2

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The Deadly Assassin (1976) is the first time any limitation on the process is mentioned, and it becomes a major plot point in almost all stories dealing with The Master from that point forward, including in the 1996 attempt to revive the series.

However...all of that predates the Last Great Time War.

The modern series has yet to nail down any limitation on the process, although it's more or less stated in "Let's Kill Hitler" that River has used up all her remaining regeneration energy, implying that there is some limitation.

If The Master can be entirely reincarnated (twice; once off-screen by the Time Lords in hopes he would help fight the Time War; once in "The End of Time"), then it seems feasible to assume that any prior limitations on regeneration might have been altered or even lifted entirely.

The upshot, therefore, is that @FredH's comment above is pretty much spot on: if the writers choose, then the Doctor can go on regenerating indefinitely. They could choose to explain the change as an artifact of the Time War; or something the Doctor figured out afterward without the Time Lords looking over his shoulder to stop him; or simply decide not to say anything at all, on the grounds that most of their viewership are not familiar with the Classic Series and won't necessarily care.

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He certainly never seems worried he's running low! –  Liath Aug 19 '13 at 13:04
    
It'd be great to see an update to this answer following the Christmas special –  Liath Apr 7 at 14:28
    
It looks like someone else provided the "update", below :-) –  Uncle Mikey Apr 30 at 17:50

In the episode The Time of the Doctor, it's confirmed that this did count as a regeneration. Between this regeneration, and the recently-revealed (Day of the Doctor) 'War Doctor' regeneration, Matt Smith, who we previously called the 11th Doctor, was in fact the 13th regeneration of that character. The math works out that the original Doctor was his original face, so the 2nd Doctor is the 1st regeneration. This then means that the 13th Doctor is his 12th and final natural regeneration.

However, just as they did for The Master, the Time Lords granted The Doctor a fresh set of regenerations (The Time of the Doctor). So as the '11th' regenerates, he turns into Peter Capaldi, the first of a new set of 12 regenerations.

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