Author's Note:

I belatedly contacted my trusty beta reader and brain-twin, and she found some rather glaring errors I'd missed. So...this has been cleaned up a bit, some grammar and tense errors corrected, and is generally more polished.

Also, she pointed out to me that non-Who fans might run into a bit of confusion. I do want this story to appeal even to those who've never heard of the Doctor, so here's a bit of explanation concerning the bits she suggested were confusing:

The Doctor travels with companions, usually humans. Some he is closer to than others, and his first companion of the new Doctor Who series was a London shopgirl named Rose Tyler. Rose was very much his soulmate, and in many ways his relationship to her was the closest he's ever had with a traveling companion. However, he lost her. She is now trapped in a parallel universe, alive and with her family, but cut off from the Doctor and the world of her birth. Shortly after this, the Doctor became involved in the rescue of a woman named Donna, who was very unhappy to have her wedding day interrupted by aliens. When it was all over, the Doctor invited her to join him in his travels, but she turned him down flat. So here he is, all alone...

"This is me, for forever
One of the lost ones
The one without a name
Without an honest heart as compass"
–Nightwish, "Nemo"

The room isn't quiet, not really. His ship is never silent, never still–and yet right now it feels silent. It isn't the first time he's felt this; he doubts very much it will be the last. Alone again, with only the repairs to his ship and his soul to command his attention. He feels as though half his self has been torn away.

All that knowledge and experience, and he still can't keep the loneliness at bay. He can't cheat death for them, or defy fate. He can't keep the walls between the universes closing, no matter how much he wants to. He can't stop them fearing him.

He sighs, leans his head back against the control panel base. Dear heaven, he's getting maudlin in his old age. Much more of this, and he'll find himself dumped on an ice planet or something, locked out of his own ship until he's in a proper frame of mind. She'd do that to him; she's done it before. He hurts, oh yes, and it is by far the worst bit in a very long time–but sitting about moaning isn't going to save anyone. There's a whole universe out there, and it wants helping.

And he's used to being broken.

One of these days, he figured he'd not be surprised to see her sitting in Wash's chair, though he didn't anticipate it'd be anytime soon. He'd given up the pretense of official piloting almost immediately, and turned it over to her. The little albatross was bidding fair to be just as good a pilot as Wash was–and without all the fancy schooling. So he let her have the chair, and pretended not to notice that Zoe avoided the bridge. Not like she was getting along real well with any sort of stairs at the moment, anyway.

He edged through the gap between stair rail and console and settled in the co-pilot's chair. "Everything clear?"

"Clear as crystal." River's long brown hair curtained her face as she leaned forward to adjust something on her own panel. "Clear as water, clear as–"

"All right, all right, I get it. No call to ramble on." Mal propped a foot against the console and reached out to toy with one of the plastic dinosaurs perched on its rim. No one had the heart to pack them away. He doubted they ever would. "Three days to Persephone, then. And hopefully," he muttered, "we ain't gonna have any trouble." It was almost a prayer, and the thought brought a wry twist to his mouth. Wouldn't the Shepherd laugh.

It was a feeble prayer, and one he'd uttered an awful lot these past five months. He didn't hold much hope of it being answered. "Things never go smooth" had long since become a personal motto.

A soft noise beside him drew him from his thoughts. River was sitting up straight in her chair, hands motionless on the console, eyes staring wide into the black. Mal frowned. Not the first time he'd seen that look. "What's wrong, meimei?"

"It's coming."

Oh, sweet hopping Buddhas. "What's coming? River? Don't leave me in the dark here, darlin'. Something's comin', you give me warning, right?"

She turned to look directly at him. Her eyes were black, the pupils were opened so wide. "The storm. It's coming."