In story terms, our characters see the symptoms and guess at the nature of his trouble, without knowing details; and always try to help him find a home in time and space. wherever he goes he tends to make ad hoc enemies; but also there is a mysterious enemy pursuing him implacably every when: someone from his own original time, probably. So, even if the secret is out by the 52nd episode, it is not the whole truth. Shall we say:
The Second Secret of Dr. Who: The authorities of his own (or some other future) time are not concerned merely with the theft of an obsolete machine; they are seriously concerned to prevent his monkeying with time, because his secret intention, when he finds his ideal past, is to destroy or nullify the future.
from the original pitch of Doctor Who (posted on Kottke yesterday).
Read the rest, including a bit about the Doctor’s morals here.