Yes, you are all accomplices to the fall, and yes, we are gone forever. Gone to a ruin so strange it must be called by another name.
The Poisonwood Bible, Barbara Kingsolver
He finds them, the lot of them, floating in space, frozen but not dead. They might be dangerous or they might not, but he saves one, because he can tell that she's different.
She wakes up on the TARDIS not long after he brings her aboard.
“There we go. All thawed out, then?”
“Who are you?” she asks, taking in her surroundings and seeming less surprised by them than he would have thought.
“I'm the Doctor,” he says, and to her credit she does not ask Doctor Who?
“Elizabeth,” she answers.
“Elizabeth! A fine, upstanding name. Now, Elizabeth, why don't you tell me how you came to be floating in space with your, uh. Your friends there.”
She looks away, closes her eyes for a moment, and there is something in her face, something so deeply sad that it troubles him in a very tangible way. “You should know that I'm not human,” she says.
“Well that's all right, neither am I,” he says, and smiles at her.
She doesn't smile back, only looks at him and stands up, slowly, as if to test her legs. But she's fine, good as new, as if she'd only taken a long nap. “You're not a Replicator. I'd be able to tell.”
“No, just your everyday Time Lord.”
She flexes her fingers and he watches, curiously. “How long were you out there, Elizabeth?”
He helps her build her human body, the way she'd planned.
It doesn't feel quite like it used to. It's better than the Replicator body, but still doesn't feel exactly like it's hers. The Doctor can offer little insight—he's never been able to go back to a familiar body. For him it is always onwards and upwards, no going back.
“You look lovely,” he tells her. “This is what you looked like before? I can see why you'd want to go back.”
She shakes her head, and it's almost sweet that he'd say so, even though- “The other body was younger.”
But in the end there's little to be said for youth, he tells her.
The first time they almost die together, it isn't Daleks or Cybermen, Replicators or Wraith. Just regular, garden variety homicidal aliens. She doesn't cower, or cry, or freeze up in a crisis—not that he expected her to, but it's a bit of a surprise just how unfazed she is by the situation.
“You found me floating in space, remember?” she says. “In a body made of nanites. I've been around the block a time or two.”
“Right. Right, I suppose you have, then.”
She looks down for a moment, away from him, the way she does sometimes, and he realizes that she's more shaken up than she's let on.
“Would you like me to take you home?” He doesn't want to ask—more than anything he doesn't want to ask, but he does it anyway.
But she looks up again, surprised, and says, “I don't have one. On Earth I'm dead, and... I'm not welcome in Atlantis.”
“Not even like this? Human, they wouldn't take you back?” He can't imagine it, anyone not wanting Elizabeth Weir.
She doesn't answer, and he doesn't press her. “Allons-y,” he says, much more softly than usual, and they go on their way.
It's not romance between them, and they both know it without having to say it. He had loved Rose, and she had loved John, and what they needed from each other was different. Someone to just be with.
She tells him about Atlantis, about rising out of the ocean, her beautiful city where she would have spent the rest of her life. She tells him about John and Rodney, Teyla and Ronon and Carson. In return he tells her about Gallifrey, silver leaves and burnt orange skies. Rose, Martha, and his dear friend, Donna Noble.
When they travel to Earth, they stay far away from DC, Colorado, anywhere someone would know her. But it's still too much to bear, and she's spent so long not crying about it, not crying about anything, that it's a shock when a tear forces its way stubbornly out of her eye. Despite her best efforts, she's crying on the TARDIS, the Doctor sitting next to her, quiet but solid.
He brushes at her cheek with his thumb. “I'm sorry. I'm sorry, Elizabeth.”
“I've lost everything,” she says, voice breaking. “I've lost my whole life.”
“You'll make a new one,” he says, and she remembers that he knows what it's like.
“You make it sound easy.”
“Oh, it's not. But you won't be alone, will you? I'm not going anywhere. I mean, I am, but you're coming with me.” He grins at her, that impossible, earnest grin, and she doesn't know how he does it, how he can keep going after everything he's lived through.
She doesn't know how she can do it, either, how she can even begin to put together a life that will bear no resemblance to the one she'd already lived. But she is alive, thanks to him, and she wonders if, together, they might just be all right.
“Yes,” she agrees. “I'm coming with you.”