Moffat told the Radio Times:
“We’ll find out that Matt Smith is actually the 13th Doctor. Although everyone knows that the Doctor can only regenerate 12 times. The 12-regenerations limit is a central part of Doctor Who mythology – science fiction is all about rules, you can’t just casually break them. So if the Doctor can never change again, what’s Peter Capaldi doing in the Christmas Special?”
Even counting the War Doctor (John Hurt), the numbers don’t add up. But remember when Moffat earlier suggested that everyone had missed a regeneration? Well, it’s related to the Meta-crisis Doctor — but not the human/Gallifreyan hybrid from “Journey’s End” himself.
When the Doctor (David Tennant) was struck by the Dalek extermination ray in “Journey’s End,” it triggered his regeneration process. Dragged into the TARDIS by Capt. Jack Harkness (John Barrowman), the Doctor channeled the regeneration energy out of himself and into his preserved hand, which was previously severed in “The Christmas Invasion.” That caused the hand to grow into the Doctor/Donna. What matters here is that the regeneration was triggered and the energy expended — regardless that it was directed outward.
In essence, the 10th Doctor regenerated into his old body. But he still regenerated. At least, according to Moffat he did. So add that to the War Doctor, and Smith gets bumped back from 11 to 13. Again, at least according to Moffat. And he’s the boss.
But why did he say back in November that he wouldn’t be renumbering the Doctors, and Peter Capaldi will be called the 12th Doctor? The answer lies in the wording of his entire sentence:
“In the script to The Day of the Doctor, Matt’s Doctor was called the Eleventh, and David’s was called the Tenth, so the numbering stays exactly the same – and we call Peter Capaldi the Twelfth Doctor.”
Sooooo… in the script for “The Day of the Doctor” the numbering stays the same. I see… That clever devil. Moffat told the truth — but only in a manner that served his purpose. Well-played, Mr. Moffat. Well-played.