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He’s not human. It doesn’t take her long to realise that the implications go way beyond having two hearts.
As if it isn’t complicated enough to handle people of your own species. That’s what Martha’s lifelong job as her family’s wartime messenger has taught her. Knowing the biology behind the workings of a brain helps squat when trying to reason with someone who doesn’t want to be reasoned with. When that someone has a brain like the Doctor’s, she can’t imagine where to start.
Sometimes he acts like a human, sometimes he doesn’t. He claims to be nine hundred years old yet he often behaves like he’s nine. He’s the last of his species and a Shakespeare fanboy. He saves worlds and condemns others, and claims that all he ever wanted to do was a bit of sightseeing.
Even during the most jarring shifts of mood she believes that there is something to be understood in the kaleidoscope of cold steel and golden grins. The logic behind the magic trick, if you will. Why she wants to know it, she’s not sure. It could be simple psychological curiosity. Maybe she thinks that if she manages to solve this—the greatest puzzle in all of space and time—he’d finally see how clever she is. It might come down to a desperate hope that maybe, just maybe, if she understood him she would be able to help him. And there it is, a budding case of her very own messiah complex, the occupational illness of medical staff everywhere. It definitely won’t be cured by the sorts of adventures the Doctor has to offer.
No matter how hard she tries, there’s only enough information for Martha to understand that there’s something she could understand. It’s like she and the Doctor are separated by a misty windowglass through which she can only see a faint, blurred-out figure. She knows he’s there, as real and solid as her, but everything beyond the general form escapes her. Over and over again she tells him to wipe off the mist from his side. He doesn’t, and the worst part is that she’s embarrassingly relieved.
Perhaps he can guess the reason; she already knows the two alternatives of what she might see and she can’t decide which of them terrifies her more. Either she is met by the gaze of a strange creature familiar only in shape (but in fact full of darkness and fire and the dust of a dead star burning billions of light years and centuries away from her Sun); or she finds out that he’s just a human with another name, as lost in the universe as she was on her first alien planet (they’re all alien to him, aren’t they?), who only enjoys himself so much because he’s already gone mad.
So she mentally prepares for all outcomes. She treats him like a regular bloke even though she knows that someday she’ll have to find someone who really is. She gives him the appropriate odd look when he kneels down to lick a bootprint, but also knows to listen when he goes on about how the aftertaste of petroleum indicates that the insurgents must be hiding at the abandoned starshipyard.
No matter his current mood, she is as ready to be kissed again as she is to be kicked out of the TARDIS, or maybe both at once. She tries not to think about which option would be better for her in the long run. He’s pondering it already and it doesn’t seem to do him any good.
At the end of the day it all works, somehow. Her return is postponed for yet another trip. She can’t claim that he owes her anything more, not after handing her the whole universe along with its history and its future.
Sometimes she wonders if all the others went through the same thought process. If Rose went. But then she stops caring because, as the materialisation noise mellows down, he’s already grabbed her hand and off they go again.