It's a funny thing, reality. (They could go a number of ways, but here's five.)
1. He doesn't fall in love because the Doctor doesn't do that, hasn't done that since Gallifrey, but here's a girl who hasn't a clue about him and he can believe—oh, he can believe—that his home planet is bright, shining, alive. No, the Doctor doesn't fall in love, but Martha Jones does and who is he to be but kind?
2. They haven't seen each other since—since she went and joined UNIT, actually. "Martha Jones," he whispers to a dark and deadly girl who hasn't any likeness to her namesake, not any at all, "what has happened to you?"
"You," she says. (You fashion people into weapons.)
3. She meets him once. It's too early. He's parked his TARDIS in the yard across her house. (Well, he says parked—crashed, more like.) She goes for a run and bumps into him. "Sorry," she tells Tall-Dark-And-Time-Lord. Martha Jones slips in her headphones, continues on, and never looks back.
4. He doesn't mean to leave her with Shakespeare, honest. He just stepped into the TARDIS, and the next thing you know he's suddenly aboard a Sontaran battleship. He hopes she likes it there, doesn't get carted off as a slave or whatever it is she was worried about. (She dies seven years later, relative time, of cholera, without her Doctor and without her family, but he needn't know that or it'd break his hearts.)
5. The funny thing is, he creates monsters and doesn't realize it. "Hello, Doctor," says the girl in dark clothing.
"Who are you?" asks the man.
"An assassin," she says, "and you, Doctor, are my target." (She puts a bullet through his head and it's surprisingly anticlimactic, because he bleeds the same as any other man, but, somehow, he's still beautiful and entrancing and she shoots him again, while he glows golden, just to be sure.)