She's gone now, he reflects sometimes when he's alone. Even as she shows up in the TARDIS time and time again and runs with him all over the universe, to him she's long dead and buried. He tried so hard not to fall for her when they met again after her death, but he couldn't help it. He's head over heels for a ghost, and every time he sees her he remembers that horrible day.
And yet she isn't really gone. Even as his time with her comes and goes, he knows they're still out there somewhere. Yes, somewhere on a planet filled with books she is dying, dying to save him and so many others. But somewhere they are sending Weeping Angels into a crack in the universe. Somewhere she is vandalizing the oldest cliff in the universe to get his attention. Somewhere, in the arms of her mother and his best friend, her story is beginning.
"You and me, time and space," she'd said. "You watch us run." Oh, how they run. And they'll never stop running, not really. He's a time traveler. He of all people knows that nobody's story ever truly ends.