Bodies are odd, and a bit cumbersome, and the Doctor has never really much thought about his as anything other than a somewhat convenient means of carrying about opposable thumbs.
Which is perhaps why upon regenerating in Miss Amelia Pond’s garden the only possible thing he can think to say to the young redhead staring at him in her nightie is, “I’m a girl!” Because it is very true, as the sudden lumps beneath his shirt make quite clear.
It’s just slightly unexpected.
Of course, it’s really not until later, after fish sticks and custard and brilliant Amelia Pond and Prisoner Zero, that he really takes a moment to look over the body he noted as he was changing in bow tie he borrowed from the hospital’s changing room.
And then he realizes this his body is no longer an ignorable vessel for opposable thumbs. It’s just very simply not right. The human ideas of gender and sex have always struck him as so antiquated as to be a bit charming, but they’re not completely unrelated to Gallifreyan notions.
“This just won’t do,” he says to the mirror, shaking his head.
He thinks for a brief moment about just declaring this regeneration a wash and trying the whole thing again, but there are bits of the body he quite likes. The length of limbs is quite pleasing and the floppy hair has a bit of rakish, cool quality. It seems a shame to toss it all out.
And are things he can do. Humans came up with ways to make the changes biology forgot about, Gallifreyans did as well. Regenerations can last for a very, very long time under certain circumstances. Far longer than anyone would ever want to be uncomfortable.
When he next sees Amelia again, a bit later than he’d planned, she says, “I thought you were a girl,” once again standing in her nightie in her garden in the middle of the night. Her hair is very bright red and the Doctor knows she wants to come.
“Momentary miscommunication,” the Doctor says, waving a hand. “The body’s not quite caught up with the mind. Give me a bit and I’ll sort it out.”
Amelia gives him a look, but there are so many other things that she cares about and that the Doctor wants to show her. The small matter of his body is the least among them. After all, what’s flesh when there’s the whole of time and space to explore with a little girl who waited a very long time?
River, however, is another story. As River often is. They’re going opposite ways, which means she logically already knows about this regeneration and the Doctor doesn’t expect her to care, because if she did it would mean something caused purposefully caused this regeneration and that would mean a great deal more the stability of time and space than he cares to think about.
River Song is an utterly maddening woman and the Doctor would never admit that he always, always wants to know what she knows.
“By the way, Sweetie,” she says as they’re working frantically to keep the Weeping Angels from killing the lot of them, “You can stop worrying.”
“You’ve got a solution?” he asks, because there is a very line between a good, old fashioned dramatic reveal and keeping things to yourself that he ought to know.
She grins, a touch frantic around the edges, but they are about to die, so he can understand that. “No, not at all,” she says breezily. “You can stop worrying about whether what you’ve got behind that bow tie matters to me.” She kisses his cheek. “It really doesn’t.”
The Doctor knows the rest is spoilers, but it’s easier to save the day anyway.