As ever, all belongs to someone with a lot more money than I have.
Spoilers for seasons 4 of Doctor Who, 2 of Torchwood and the events in the movie Serenity.
I will be using events from all parts of the Firefly 'verse in this story, including the comics, but that's because there is limited canon to work with.
With thanks to jpdt19 for beta-reading it for me and fixing some of my grammar to help it flow.

The Sleeper Awakens
Part 1: The Good Captain

Persephone had changed a lot over the years, but thankfully the Eavesdown Docks were still as disreputable as ever. He needed that, cash-in-hand and no-questions-asked. What he really needed was a ship headed out from the Core, out to the border planets. Out there the Alliance's grip was weakening, following the recent revelations about their ill fated experiment on Miranda. It was this sudden and unexpected upheaval that had given him the chance he needed to escape from the Alliance research center and make a run for it. All he needed to do was get back to Woodstock; he had a ship stashed there with a working hyper-drive, assuming that no one had found it in the years he'd been away.

It had been twenty, maybe thirty years since he'd found this system and decided to stay a while. He was still technically a Torchwood operative, but he hadn't seen a pay check in a hundred years. Still, they had a way of finding him when they needed use of his 'special' talents. It seemed however that this one system, so far off the beaten track yet teaming with life, was the one place he'd found in all of time and space where neither Torchwood nor the Time Commission was willing to follow him. Evidently there were some secrets that even they wanted kept hidden.

He looked at the line of waiting ships, first working out which were headed in the general direction of Woodstock, then ignoring the two that looked a little too clean and respectable. He stopped dead when he saw the next: a Firefly class transport, the kind of ship that would fly forever if the mechanic knew what they were doing. He'd spent a lot of time on Firefly's over the years, and had grown quite fond of them. Smugglers and other disreputable people liked them for their unobtrusive demeanour and dozens of hard to find hiding places that could easily be over looked by someone who didn't know what they were looking for. That was exactly what he needed: a ship that wouldn't warrant a second glance at most customs stations, if it ever decided to pass through one. He looked up at the nose and felt a momentary chill run down his spine as he read the name: Serenity.

It had been a while since he'd heard that name, but his memories of the past few years were so jumbled and unfocused that he couldn't say for sure how long it had been exactly. All he knew was that the Alliance knew he couldn't die, and wanted to find out how and why. The fact that he wouldn't stay dead only meant that they could cut on him and hurt him as much as they liked, sometimes just to see how much he could take. He hadn't broken, he was sure of that. He wasn't sure how; maybe he'd been through so much already that there was nothing left that they could do to him.

Serenity, that's where nightmare had started, The Battle of Serenity Valley on Hera. The Alliance had come rushing in like a tidal wave, only to break against the Independents defences. That had been one of the proudest moments of his life: holding out against the full might of the Alliance for seven weeks, two longer than High Command had managed before surrendering. He hadn't been there at the end: the Alliance had seen what he could do and managed to grab him and get him off planet before the white flags had been shown, but they had been kind enough to inform him during one of his more lucid moments. They'd even shown him photos taken from orbit; soldiers, Browncoats and Purplebellies alike, still dying while their leaders hammered out the terms of the surrender. The bastards had even laughed, joking that you didn't have to pay dead troops. They'd wanted to break his spirit, but they didn't fully understand just who they were dealing with.

"Need a hand there, mister?" A cheery voice asked, "We're headed for Dyton Colony."

"I need to get to Woodstock, and that's only a few moons over," he said, as he turned to see who had spoken. It was a young woman. A very attractive young woman, at least underneath the layers of oil-stained cloths she wore. Smiling broadly he instinctively offered his hand.

"Harkness, Jack Harkness," he volunteered.

"Kaylee." The woman, smiling back, took the proffered hand and shook it, "So, Woodstock? Not much out there but a few mines and a couple of ranches."

"I have friends out there who I've not seen in a while." Jack kept his smile warm, not wanting to give away too much, "So, how much for Dyton..." There was the unmistakable click of a pistol being cocked right behind his head. He froze, and felt a hand reach round under his coat and pull free the gun he'd taken from one of the Alliance guards when he'd made his escape out of his waistband.

"You treat all your passengers like this?" He asked with more than a little sarcasm, "Or just the good-looking ones?"

"No, just the dead ones." A familiar voice snapped, "Inside. Kaylee, get the door."

"Captain?" A look of confusion fell upon the young mechanics face, but she hurried to comply while Jack was marched at gunpoint into the middle of the cargo bay.

"That's far enough." The voice commanded, "Zoë, get in here right gorram now!"

"Hi Mal, long time no see." Jack slowly turned round to face his former comrade-in-arms, "Is this how you treat all your former commanding officers?"

"Jack Harkness is dead; I saw him get his head blown off in Serenity Valley." Mal Reynold's voice was cold and hard, matching the look in his eyes, "So why don't you tell me just who the hell you are and why I shouldn't fill you full of holes right now?"

"Well, I'd hate to ruin a good shirt..." Jack smiled, trying to defuse the situation, "You've got a lot of questions, I can understand that, but I don't have the time to answer them right now. I need to get off planet before the Alliance catch up with me, so either take me as far as Dyton or I'll find another ship that will."

"Captain, what in the hell is going on?" Zoë appeared in the hatch that led through to the infirmary, but stopped dead in her tracks when she saw who else was standing in the cargo bay, "Ching-wah tsao duh liou mahng!"

"It's good to see you too, Zoë." Jack smiled at her over his shoulder, "Can't say I'm surprised to see the two of you are still together."

"We're not together." Mal snapped, "Now shall we get back to who you really are, or do we jump right to the filling you with holes part?"

"I'd rather you didn't, if it's all the same with you." Jack slowly lowered his hands, "I know you have no reason to trust me, given what you saw, but it's really me." A cocky a sly smile, "Who else would know what really happened that time you got drunk on Apollo during R&R, or what that tattoo said before you had it removed."

"Tattoo?" Zoë asked, one eyebrow raised, "What tattoo's that, Captain?"

"The tattoo he used to have on his left shoulder." Jack's smile widened to a grin. "The one with the red rose and 'mother' written below it."

"Son of a..." Mal lowered his gun, "I saw you die."

"The Alliance … did something to me, brought me back." Jack's smile faded, "I guess they can't remember how they did it, as they've spent all the time since trying to work it out."

"The Alliance is after you?" A worried expression flashed across Mal's face, "Kaylee, is everyone back aboard?"

"Yes captain; we were just waiting on you and any passengers." The mechanic nodded slowly, "River said we're ready to go as soon as you give the word."

"Consider it given." Mal re-holstered his gun, but kept a tight grip on the one he had taken from his former CO, "I want some space between us and this planet before the damn Feds come looking for Captain Harkness here."

Kaylee disappeared up the ladder without a word while Zoë crossed the deck to get a better look at Jack.

"You look good, for a dead man," she commented. She was clearly still not sure if she trusted him, and looked to Mal for advice, "What do we do, sir?"

"We go to Dyton, as planned; we've got legit cargo this time, and I don't need some merchant going crying to the Feds because we went AWOL with their goods." Mal didn't take his eyes off of Jack, "As for him, well, that's a whole other kettle of fish; I say we make him have a little sit-down with River once we're in the black and see what she says."

"You sure that's wise?" Zoë asked, "I know she's more stable these days, but still..."

"Way it is is the way it is." Mal shook his head, "I've got a boat load of questions, and that girl's the fastest way of getting truthful answers. Unless you want to have Jayne do the asking?"

"River's a better idea." Zoë agreed, "But what do we do with him till then?"

"Go find the Doc." Mal grabbed Jack by the arm and frog-marched him towards the infirmary, "I want to make sure this really is Jack Harkness."

With the exception of a powerful spotlight pointing straight down to the middle of the dais, the room was totally dark, as was befitting a room that did not exist. The men sitting behind the high desks knew each other's dirty little secret, and thus kept them by mutual consent. Entry to the room was strictly controlled, for it was home to the Alliance Special Security Council, the unelected body made up of members of the senate, armed forces and other more shadowy agencies linked to the government. All the plots and counter-plots, all the words whispered and knives in the dark were theirs to unravel and employ as they alone saw fit, far away from the public eye. They were the New World Order, and they were very unhappy.

"Please, explain to us how he managed to escape from our single most secure Research and Development complex?" A voice asked out of the darkness, its owner's identity disguised electronically, "And then managed to elude pursuit and, one mustpresume, manage to escape from Londinium itself."

"Security at the complex had grown complacent and lax." The senior of the two Operatives standing in the middle of the dais kept his eyes locked straight ahead, "The recent political upheaval after the Miranda indecent resulting from the ongoing Tam case created the perfect opportunity for the subject to effect an escape. While we know so little about his true history, it is worth remembering that he is an exceptional fighter and an experienced confidence trickster and thief, all skills that he displayed during his escape. Add to that the rather unique ability that led to his relocation to the research complex in the first place..."

"Yes, we are all very well aware of Mr Harkness' past exploits, and the danger he represents given what he can do." A second distorted voice broke into the conversation, "We will have time to go over it again once he is back in our custody. Until then, our main concern must be his containment and recapture."

"Agreed," the first voice replied, "You have your mission, and our full support. Use whatever means you must to recover Mr Harkness and silence anyone who he has confided in. The government has been shaken, but still stands; we can not risk another Miranda!"

"As you wish." The lead operative bowed his head respectfully, "We shall begin our search at once."

To Be Continued...

Off on holiday soon, so don't expect anything more until I get back.

Chinese/English translations (with thanks to the Firefly-Serenity Chinese Pinyinary):
Goram God-damn
Ching-wah tsao duh liou mahng frog-humping son-of-a-bitch.