In the most recent issue of Doctor Who magazine, Steven Moffat asked:
“Here’s a question I tried on some Doctor Who fans recently, and we were all a bit startled by the answer, when it finally emerged – if we got it right. Okay; keeping in mind that everything you know for sure is probably wrong, answer me this: in which story is it confirmed, definitively, that the Doctor is not human?
“Now before you jump up and yell An Unearthly Child – sorry, but wrong. He makes it clear he’s not from this time, and seems to indicate that he was born on another world, but he never says he’s an alien. He could, just as easily, be a human being from the far future, born on some colonised world. Indeed, most of his conversation in the early days would seem to confirm that he thinks of himself as human, and he even explicitly states that he is, at least once.
“So come on then. To your DVD collection. In what story do the wise men and women of the BBC stop fudging the issue, and make our hero Not One Of Us. I’m not talking about him having remarkable abilities or attributes – we’ve always known he’s not ordinary, that s fair enough. Spider-Man’s not ordinary, but he s not an alien. And I’m not talking about series bibles, or internal memos or retconned continuity – when did the Doctor Who production team stop hedging their bets and make him alien?"
We might well wonder or speculate about his motivation for asking such a question, nevertheless, I shall offer a straight answer.
The first time the Doctor is definitely identified as non-human is in The Dalek's Master Plan. Mavic Chen discusses the Daleks' opponent:
CELATION: Having had your contribution to this great weapon stolen, it must be a relief to you now that the Daleks have managed to recover it.
CHEN: Without my help, it is unlikely that they'd have got it back.
TRANTIS: At least that absurd story that it was my people from Trantis who stole the taranium has been discredited.
CELATION: Yes. They were from Earth, I believe.
CHEN: Only two of them and they are under the influence of some creature from another galaxy.
TRANTIS: He looked like an Earth creature.
CHEN: That's only a disguise. The Daleks know of him. He is some kind of time and space traveller.
CELATION: Then he is nothing to do with me. We have not yet conquered the dimension of time.
CHEN: I hear your experiments in that field are progressing, Trantis.
TRANTIS: We have not yet succeeded. Only the Daleks know how to break the time barrier.
CELATION: And this other creature, from wherever he comes.
Here the Doctor is described as a 'creature from another galaxy' who only appears to be human. The notion that the Doctor's human appearance is only a disguise is a fascinating one. What does he really look like? A walking jellyfish? A purple spider? It's rather unfortunate that later stories have not followed this idea. The only exception would be the novel Sky Pirates!, in which the Doctor transforms into his 'Other other self,' a sort of cosmic god-being.