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An incarnation is a physical form of a Time Lord, which means the first body and the regenerated forms of a Time Lord count as an incarnation.

The first regeneration cycle of a Time Lord contains 13 incarnations until that Time Lord dies, except in rare occasions. Additionally, in the "Kill the Moon" televised story, The Twelfth Doctor mentioned that he doesn't know how many times he can further regenerate, making the second cycle unknown in terms of incarnation limit.

This word is often mistaken by "Doctor", when fans talk about the Doctor's regenerations, because of John Hurt's War Doctor (Day of the Doctor) and David Tennant's alternate Meta-Crisis Doctor form (Journey's End) which both still count in the regeneration cycle. The term "Doctor" is only used in specific situations and only the Doctor chooses to name himself with that term, like he mentioned in "Time of the Doctor" - "Doctor" is the name he chose, it was sort of a promise he made to himself, to help the others in need (never give up, never give in).If an incarnation doesn't fit the role of the Doctor, then the Doctor doesn't count it as one of the Doctors, but as an incarnation of its body because he wasted regeneration energy in the regeneration counter.

So, in a simple example:

William Hartnell: 1st Incarnation - 1st Doctor

Patrick Troughton: 2nd Incarnation - 2nd Doctor

(...from Jon Pertwee to Paul McGann, the counting is similar)

John Hurt: 9th Incarnation - War Doctor or "The Warrior" (it doesn't count in the Doctor's list because of his actions in the Time War and he doesn't remember his good actions either, so the Doctor left his definition as The War Doctor, the Doctor title is just an euphemism because in the end he made the right choice instead of the previous wrong one, but it was only because his future selves helped him)

Christopher Eccleston: 10th Incarnation - 9th Doctor (The Doctor counted this form as a Doctor again because he kept the promise made by himself. The incarnations always count in the regeneration cycle and they don't change.

David Tennant: 11th Incarnation - 10th Doctor

David Tennant: 12th Incarnation - Meta-Crisis Doctor (this form was made because the 10th Doctor (David Tennant) had "vanity issues" like the 11th Doctor (Matt Smith) mentioned in "Time of the Doctor" and it diverges from the original body of the Doctor in physical form and in a death without a regeneration and committed genocide, making this form an Incarnation, because it counts in the regeneration cycle, but not one of the Doctors)

Matt Smith: 13th Incarnation - 11th Doctor

************************************* FIRST REGENERATION CYCLE IS OVER ***************************************

******************** SECOND CYCLE GIVEN BY THE TIMELORDS (Time of the Doctor) ***********************

Peter Capaldi: 14th Incarnation - 12th Doctor (first in this new cycle)

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