It's best to think of this as a Doctor Who story set in the Firefly universe. There is little interaction between the 11th Doctor and Clara and the crew of Serenity, though they do cross paths from time to time. This story builds on earlier fanfiction, but can be read independently. You'll find a summary of the earlier stories in the note at the bottom.
The TARDIS control room was empty and, aside from the usual time rotor engine hum, it was silent.
It was silent for a long time. Days. But finally the TARDIS shuddered slightly — in anticipation? — and the silence was broken as the doors creaked open and the Doctor and Clara entered, continuing a brisk conversation that had started upon taking their leave of George Washington.
"And so that's what happens," the Doctor said, "when a distant power tries to enforce their will on an independent-minded people. They squeeze and and they squeeze until the colonists, peaceful though they may be, turn to war."
"I thought George was pretty decent," Clara opined, her face thoughtful. "I quite liked him. Thomas was a bit brusque, though."
The Doctor stared at her. "Decent? A bit brusque? Is that all you have to say about two of the most famous men in Earth's history?"
"Well, in the end they're just blokes, aren't they?"
"Just blokes," the Doctor repeated.
"They both hit on me," said Clara.
The Doctor was stunned. "They never."
"Oh, you're so pretty," said Clara, raising her eyes skyward and clasping her hands to her chest. "I've never met a girl like you. If you accompany me to my home, I'll show you my copy of the Declaration of Independence."
"Right," said the Doctor, clapping his hands together and moving to the console. "On that note it's high time we got you back home."
As he worked, Clara studied him. "Just what is it with you and hats?" she said.
The Doctor was wearing a black hat, triangular shaped, with gold trim along the edges. He took the hat off, bowed with a flourish, then replaced the hat.
"I wear a Tricorn now," he said, tugging on the lapels of his coat. "Tricorn's are cool."
As Clara shook her head, the Doctor pulled the dematerialization switch and the TARDIS slipped into the time vortex.
With the familiar sound of dematerialization, the time rotor rose and fell and the Gallifreyan symbols above the console rotated. Clara stared at them, fascinated. She was about to ask the Doctor a question when the TARDIS began to shake violently, knocking them off of their feet. The cloister bell rang briefly, then all was still and silent.
Clara got back to her feet while the Doctor, still on his back, propped himself up on his elbows and stared, first at his hat, which lay on the floor beside him, and then at the console. The rotor was motionless.
"Doctor, are you alright?"
Getting to his feet, the Doctor nodded but then lurched backwards and said, "Ow."
Clara's eyes widened, but he smiled and set her mind at ease. "I'm fine," he said. "Just received a message, but it delivered a heck of a wallop."
Pulling out the psychic paper from his inside coat pocket, the Doctor flipped open the cover.
"What is it?" Clara asked, coming beside him.
The Doctor, his eyes wide, looked at Clara. After a moment he whispered, "It's a message. From another universe."
"Another universe? How's that possible?"
"It isn't. It shouldn't be."
"Well, what does it say?" Clara asked.
Staring at the message again, the Doctor said, "It's space time coordinates. But they're fuzzy, probably garbled while traversing the boundaries between the universes. And there's a word. Just one word. Miranda."
The Doctor and Clara looked at each other.
"A message…" Clara began.
"... from another universe!" the Doctor said, his face now full of giddy delight. And with that, he darted to the console and began to dance about, pulling levers, pushing buttons, and entering coordinates.
"You can do that?" asked Clara. "Travel to another universe?"
Sparks flew from the console, showering them both, and the Doctor grinned widely. "With great difficulty," he said, over the noise of the TARDIS. There were clangs, crashes, and great shudders as the Doctor continued to work, and then… nothing.
"What's happened?" Clara asked.
The Doctor, a look of disappointment on his face, said, "She doesn't want to do it, and I can't quite coax her."
"Hmmm," said Clara. Then she walked up to the console and gave it a good kick.
"Silly old cow," she said, as the Doctor gaped at her. "I knew you couldn't do it, you sad excuse for a TARDIS."
There was a great shudder, causing Clara and the Doctor to grab hold of the railing for support, and then the time rotor began to rise and fall as the cloister bell rang and the TARDIS shook like a circus ride.
The Doctor blinked. "You — You insulted my TARDIS. You kicked her."
"Just gave her a little nudge is all," Clara said.
Moving carefully to the console as the TARDIS shuddered and groaned, the Doctor patted the instruments and said, "There, there, old girl, she didn't mean it."
A few moments later there was one last shudder and it was over. The Doctor and Clara looked at each other.
"Well, Clara Oswald," said the Doctor, "are you ready to see another universe?"
In way of answer, Clara cocked her head slightly then walked to the door and opened it.
The TARDIS had materialized on a hillside near a wind turbine farm. In the valley below there was a town with roads radiating outward from a central multi-story building. Other buildings were mostly single story, flat-roofed affairs. Orchards ringed the town while farmland stretched further into the valley. They could make out people milling about, particularly in the centre of town.
Using his sonic screwdriver, the Doctor scanned the area.
"These are humans," he said, "but we're not on Earth. The gravity's isn't right. An outpost somewhere, then."
"Earth?" Clara said. "You mean there's an Earth in this universe?"
"Most likely. This universe may be quite similar to ours, but different choices will have sent them in different directions."
The Doctor flipped the sonic in the air, caught it, then placed it back in his coat pocket. "Let's see what we can find out, shall we?"
On their way, Clara said, "They're able to colonize another world but they still have wind farms and overhead power lines."
"Good for you, Clara. Also note the hodge-podge of building materials and styles. It's possible that these people were transported here, then left to their own devices."
"Maybe that was by choice," Clara said. "Some people prefer to live as their ancestors did."
The streets were simply packed-down earth, and dust was everywhere. And so, remarked Clara as she wiped her nose, was the smell of unwashed bodies.
"Now, now, Clara. Don't be unkind. Water could be a scarce resource on this planet."
Clara and the Doctor wandered about, noting that people were dressed simply, in a variety of styles, and seemed healthy and fairly happy. It must have been market day, unless stalls and vendors were the norm here, with table after table of crafts, utensils, and clothing. A cacophony of sounds assailed their ears as vendors hawked and bargained with customers.
Once in a while, a group of children would dart out, laughing and chasing one another. After one such group sped past them, nearly bowling the Doctor over, Clara felt something hit the back of her head. As she rubbed her head, Clara saw a rubber ball come to rest nearby. She picked it up and looked behind her at the gang of children, some of whom wore expressions of fear, while others laughed and pointed at her.
"Oi! You lot!" She said. "Which one of you rascals threw this?"
"He did!" They all said, pointing fingers at each other.
"I see," she said. "It's like that then, is it? How about a taste of your own medicine then?"
With that, Clara drew back as if to throw the ball right at them. The youths started to back away. "She wouldn't," said one. "She might," said another. "Just look at her, she's going to do it," said a third.
Clara suddenly threw the ball upwards so that it sailed far above the rooftops then arced back down, landing right in the thick of them. The boys cranes their necks, shielding their eyes from the sun, then one of them caught the ball and brandished it, whooping for joy. Clara smiled and turned to look for the Doctor. While she had been occupied with the boys, the Doctor had wandered ahead and was speaking to a vendor. "Oh no," she said, and dashed forward. Too late. The Doctor was trying on something that bore a striking resemblance to a fez.
"Doctor," said Clara, a note of warning in her voice.
Turning to her with a wide grin, the Doctor said, "Perfect, don't you think?"
"Perfect," Clara repeated. "Such a shame you haven't any money with you."
His grin faltered for a moment, then a look of triumph lit the Doctor's face and he pulled a yoyo from one of his coat pockets.
The vendor was an older man with thin white hair, round rimless glasses, and dressed in a well worn khaki shirt and trousers. Regarding his customer with curiosity, his eyes widened as the Doctor demonstrated the yoyo.
"I haven't seen one of those since I was a boy," the man whispered with wonder in his voice.
"A fair trade for the fez?" The Doctor said.
"More than fair," said the man as he reached for the yoyo, then caressed it like a favourite child.
Rolling her eyes, Clara strolled past the Doctor until she spotted a book vendor. There she stopped and began to peruse the wares.
"Anythin' I can help you find, dear?" said the elderly woman seated on the other side of the table.
The Doctor joined Clara and said, "Some history perhaps. Always enlightening, history." The Doctor flashed his best grin, but the woman's smile turned slowly to a frown.
"Depends, don't it?" the woman said. "This here's a history book," she said, picking out a book with a red-leather cover and handing it to Clara. "For all the good it'll do you. It's approved by the Alliance, as are all history books, else they ain't published in the first place."
Clara and the Doctor shared a glance. The woman had practically spat out the word, "Alliance".
Clara passed the book to the Doctor and they made brief eye contact. As he perused its pages the Doctor said carefully, "They do like to keep a lid on things, don't they?"
"Ha!" the woman spit out. "Nothin' they like better than tellin' God fearin' people what to think, even way out here. Can't just mind their own business and let us mind ours. Fought a whole war, didn't we, though much good it did in the end. All those people dyin' and for what?"
"What indeed," Clara said. "Bet it seems like yesterday that the war ended."
"''Deed it does, though it were years ago now. Lost a husband and son. Most folk here on Lilac lost someone. What about you?" she asked.
"I lost everyone," the Doctor said.
"Sorry to hear it," the woman said, shaking her head. "Were you a soldier yourself? You seem a might young."
"I'm older than I look," said the Doctor, smiling wryly. "And in the war… well, I did what was necessary. It does seem at times that it wasn't enough."
Nodding, the woman said, "Listen, you keep that book if you like. You'll see, the history it tells ain't nothin' like what we folk remember."
"Very much obliged," said the Doctor, nodding to the woman. "Just one last question. Does the name 'Miranda' mean anything to you?"
Shaking her head, the woman said, "'Fraid not. Don't know any Mirandas 'round these parts."
After taking their leave, the Doctor read as he walked, ignoring the helter-skelter of people on the street. Then he closed the book and said to Clara, "There is an Earth in this universe, but it's been abandoned. Humanity since established itself in this solar system. The government is located in the central core. There was a war when the outer planets declared independence."
"That doesn't sound familiar," Clara said.
"Those who ignore history…" The Doctor began. "Hmm. I wonder."
"Do they know their own history?" Clara pondered.
"I'm not sure. In here, they refer to Earth as 'Earth That Was'. Perhaps they lost their history after whatever event prompted their migration here."
Clara's attention was caught by a sound further along the road and she tapped the Doctor's shoulder. A flying vehicle, coming from the other direction, came to rest at a building up the street from them. Four people disembarked and then entered the building.
"Perhaps they're with this Alliance," the Doctor said. "What say we wander in that direction and see what they're up to?"
Upon reaching the vehicle, they examined it with interest.
"It's certainly well used, don't you think?" Clara said. "All dusty and scratched."
"And constructed from a hodgepodge of parts, like these buildings. Likely not an Alliance vehicle after all."
With unspoken agreement, they started for the doors of the building, but stopped short upon hearing gunfire from within. Then there was another sound, and they looked up. Two ships were descending rapidly. On the street, people stopped and stared and pointed. In short order, the ships came to rest, hovering over the rooftops.
If the town's buildings and the flying vehicle had seemed like a hodgepodge of parts and materials, these ships took the cake, covered as they were with odd protuberances and haphazard splashes of colour.
"Well, they win the prize," Clara said. "These are definitely the ugliest ships I've ever seen."
The Doctor started backing away. "I've a feeling we may have more to worry about than their appearance."
Moments later, rappel lines dropped from the ships and people descended to the ground. Clara just had time to think that there was something odd about their appearance before all hell broke loose.
"Reavers!" several people called out. This was immediately followed by screams and a mad scramble to get off the streets.
Clara and the Doctor backed away, round the corner of the building and hopefully out of sight.
"Are they… human?" Clara asked.
The Doctor didn't answer, riveted as he was to the commotion.
Clara clapped a hand to her mouth. The Reavers were slaughtering the locals. Wait, not only slaughtering…
"Doctor, they're… they're eating these people! Oh, I think I'm going to be ill. We have to do something. Doctor?"
His face pale, the Doctor said, "There's nothing we can do, Clara. We'd be killed like the rest."
Just then, the four who had arrived on the flying vehicle dashed outside with bags and a case, making a hasty exit. A woman boarded first, then a younger woman, helped by a man in a long, brown coat. One man sat up on the vehicle's railing with a rifle at the ready, scanning for threats.
"That girl," the Doctor said.
"What?" asked Clara. "What about her?"
For a moment, the girl turned her head, making eye contact with the Doctor, an expression of interest on her face. Then the vehicle set off, and a young man dashed from the building towards it. "Take me with you!" he screamed as he tried to clamber aboard.
The man in the coat hesitated, then pushed the man off. "Get back in the vault with the others!" he called out. But the man didn't make it back inside. Three Reavers had grabbed him and were dragging him away. Brown coat took aim with a pistol and shot him, then the vehicle sped off. The Reavers dropped the dead man, seemingly in disappointment.
"Oh my God," Clara said. "They only eat their victims if they're still alive. Oh, I think I'd rather face the Daleks than this."
"We need to take cover," the Doctor said, grabbing Clara by the arm. "We've been spotted."
Glancing behind her, Clara saw a group of Reavers rushing towards them.
"In here," the Doctor said, as they pushed through the doors. "One of them mentioned a vault."
It was dark inside, stark, with a stonework floor, some floor to ceiling pipes, shelving units with jars and carvings, and a raised area at the back with a counter and units of wooden drawers.
"There's no vault here, Doctor," said Clara.
Scanning the room with his sonic screwdriver, the Doctor let out a "Hah!", then opened a compartment and pulled a hidden lever.
"It's jammed," said the Doctor. "Or locked from the inside."
Again he used the sonic, and a hole in the floor opened, revealing stairs leading below. Just then, the outside doors burst opened and a half-dozen Reavers entered, snarling and snapping their teeth.
Ushering Clara down the stairs first, the Doctor followed, then used his sonic to lock the vault from within. After wiping his brow, he descended the last few steps.
They stopped abruptly at the bottom of the stairs. A young soldier was positioned directly in front of them, his eyes blinking rapidly and his face dripping with perspiration. He was barely able to steady the rifle pointed in the Doctor's direction. There were perhaps a dozen people behind the soldier, mostly men, but a couple of woman and a little girl, perhaps five years old. A few were moaning and crying and clutching each other. One man was sprawled unconscious on the floor.
After observing all this, the Doctor raised his hands and said, as gently as possible, "We're not here to hurt anyone. We're just taking cover from… what's out there."
"We're not one of them," Clara said, to reinforce the Doctor. "We're just like you."
"Well," said the Doctor, turning to Clara, "not just like them."
"Shut up Doctor," said Clara.
The soldier looked at them closely, then breathed a deep sigh and went to sit on the floor. He trembled, hugging himself.
"What are they?" Clara said. "Out there."
"Reavers," someone spat out.
"They're human," the Doctor said.
"They're not human," one of the women said. "They may have been once, but those… things are not human."
The other woman was seated on the floor, knees pressed against her chest, rocking back and forth and trembling, her eyes wide and sightless. The girl, apparently the woman's daughter, was stroking her mother's hair and patting her shoulder, despite her own tears and shudders.
The Doctor approached the girl and knelt down. She wore a plain dress decorated with butterflies, socks that had once been white but were now the colour of sand, and scuffed shoes with open toes. Her dark brown hair was thick and curly with ringlets falling to her shoulders. The dirt on her face was smeared with tears.
"You are a brave girl," the Doctor said with a smile. "You're perhaps the bravest girl I've ever seen."
After swallowing a couple times, the girl said with a small voice, "I'm not brave. I'm scared."
"Being brave doesn't mean you can't be scared," said the Doctor. "It means thinking of others even though you're scared. And here you are, scared, but trying to help your mother just the same."
The girl's deep brown eyes made contact with the Doctor, but she said nothing.
"Tell you what," said the Doctor. "Such a brave girl deserves a reward. Now this hat," he said, removing his fez, "is a very special hat. I want you to have it to remind yourself that if you ever feel scared again, you are in fact a very brave girl."
He placed the fez in the girl's hands. She put it on her head, wiped her nose with her sleeve, and smiled.
"Thank you," she said, and hugged the Doctor's neck. Then she turned back to her mother, patted her on the shoulder, and said, "Don't be scared, Mom. I'm here."
Getting to his feet, the Doctor rejoined Clara. She looked at him appraisingly then said, "I knew there was a reason I loved you," and gave the Doctor a big hug.
It was over an hour later that they received the all clear and opened the vault door. On the street, people shuffled about, their faces white with shock. Sometimes they bumped into one another, then shuffled off, wordlessly, in another direction. The only sound was that of weeping. Bodies, and parts thereof, were strewn helter skelter.
"Is this why we were called here?" Clara asked. "To stop these Reavers?"
"I don't know," the Doctor said. "But I promise you, whatever the reason for that message, we will get to the bottom of it. And I would be very surprised if it didn't have something to do with what's happened here."
With that, the Doctor took out his psychic paper. "The spacetime coordinates are clearer. Perhaps because we've been in this universe for a while. I know where we have to go."
Retracing their steps, Clara and the Doctor walked back through the eerily quiet streets that so recently had teamed with life.
"These poor, poor people," said Clara. "We were just rubbing shoulders with them… oh no."
Clara stopped beside a severed arm. There was no sign of the body to which it belonged. The skin was pale, with age spots and tufts of coarse grey hair. The hand was wrinkled, the nails long and dirty, and the fingers still clutched a yoyo.
They continued along the street in silence, until the Doctor's eyes widened and he tried to avert Clara's gaze. But her curiosity overcame her. She looked, then dropped to her knees and stroked the hair of two boys, not more than twelve years old, their faces and clothing soaked in blood. Their throats had been slit haphazardly with a jagged blade. Near the boys lay a blood-soaked rubber ball.
Clara wiped a tear, then her eyes narrowed, her lips pursed, and she stood. "Let's go Doctor. Whoever is behind this is going to be very very sorry we were called to this universe."
In "Goodbye", Mal and company learn that the Alliance has been experimenting with time travel. Determined to put a stop to further Alliance meddling, they destroy the equipment and kill the inventor. Despite their intercession the work continues, and over the course of the next 50 years time travel technology is perfected. However, there is dissension in the ranks of the future Alliance. After a clone of Mal is inserted into the 20th Century, a rogue operative travels back in time to kill Alexis Castle, the daughter of Mal's clone. In "A Firefly in the Castle", Mal is recruited by the future Alliance to intercept the operative and save the life of his niece. A few years pass, then, in "Castle Serenity", Richard Castle and Kate Beckett are brought into their future to help Mal and his crew prevent an atrocity planned by former Browncoats. While disguised as Mal on Beaumonde, Richard Castle has a brief encounter with a tall, gawky man dressed in a long frock coat and bow tie.