Realized the other day while rewatching End of Time: the Doctor’s utter freakout at the climax of Utopia, when Martha tells him the professor’s got a fob watch. I always figured he guessed right off the bat that if another Time Lord survived, of course it would be the Master—his own personal bad penny, turning up once again.
That still never quite explained the blind panic with which he delivers that line in the title though: “Brilliant, fantastic, yeah. But they died, the Time Lords, all of them, they died!” Okay, yes, that is a nicely impersonal way to say “But I killed them, all of them, I killed them,” and so if Yana’s a Time Lord then the Doctor’s got some ‘splaining to do… but still. The intensity of the panic and fury there is weirdly disproportionate, less “it must be the Master and he must be up to something and I’ve got to stop him” and more “the world just crashed down around my ears and if I don’t get up there RIGHT NOW it means the end of absolutely everything.”
And then it clicked as I was watching EoT. Ten making all his pretty speeches about how he never would, and he won’t take a weapon, and he must be better than the Master even at the cost of the human race… and then the instant he finds out the Time Lords are back, he grabs Wilf’s gun and charges into the breach, because every item on his priority list has just been superseded by “Make sure the Time Lords stay dead.”
The Doctor in Utopia isn’t afraid that Yana will turn out to be the Master. He’s afraid Yana WON’T turn out to be the Master. The Master he can deal with. What he’s really afraid of is what the rest of the Time Lords became.