Title: Armageddon

Rating: T

Warnings: Major spoilers for "Utopia", "The Sound of Drums" and "The Last of the Time Lords"; violence; mild language

A/N: This is a sequel to "Beauty, the Beast" and I have to say I am quite proud of that story. Many, many thanks to everyone who read/alerted/favorited/reviewed "Beauty, the Beast". I thoroughly enjoyed myself writing it and I am happy to announced that I *plan* on writing many more sequels in this universe as well.

But first, how 'bout I get to the story at hand. This is a SLIGHTLY AU version of the events in "Utopia" "The Sounds of Drums" and "Last of the Time Lords". I say slightly because it is definitely going to end pretty much exactly the same, however, I've added Spencer Reid into the TARDIS and I will spend a great deal of time showing Martha's journey during those last episodes as well.

It starts off at the beginning of "Utopia", directly after the events of "Beauty, the Beast".

The main focus, of course, is Reid, the Doctor, Jack and Martha's family on the Valiant with the Master and Martha's journey across the world (which is how she would meet said people). Basically I decided showing Martha's journey in more detail is a good opportunity to toss CBS characters and BBC characters into this post-Apocalyptic universe. (An idea given to me by KMW1968 which I have grabbed onto whole-heartedly.)

So, as a side note, this fic will contain cameos and larger appearances from the rest of the BAU (Hotch, JJ, Garcia, Morgan, Prentiss, Gideon and/or Rossi), members of the NCIS team (Gibbs, Tony, Ziva, Abby, Ducky), members of Torchwood (Gwen, Owen, Tosh, Ianto), members of the CBI (Jane, Rigsby, Lisbon, Cho – this is set before Van Pelt's time, unfortunately, but I may include her anyway) and members of Sherlock (Sherlock, John, Mycroft, Lestrade, Molly, etc.)

If you haven't seen/don't watch these shows don't worry too much about spoilers. I promise not to give anything away and if you don't know the characters you can treat them as OCs, just understand that they aren't mine, they are the creations of someone else entirely.

Please review! (And I apologize for the long a/n)

Armageddon:

Part I: Utopia

Chapter One

The TARDIS engines whirred loudly as she landed just outside of the Millennium Centre in Cardiff. Reid and Martha watched, confused smiles on their faces as the Doctor practically danced around the controls, pulling levers and pressing buttons.

"So, what are we doing in Cardiff?" Martha asked, "Bit tamer than I'd expect from you."

"Ah, well you see, the thing about Cardiff is it's built on a rift in time and space… It's like, California and the San Andrea's fault. The rift bleeds energy and every now and then I open up the engines, soak up the energy and use it as fuel."

"So the rift is like your own personal gas station?" Reid asked, raising a brow.

"Exactly. Should only take about… hmm, twenty seconds," The Doctor said, pausing with a surprised look on his face. "Ooh, the rift's been active."

Martha frowned, something nagging in the back of her mind. Suddenly, she remembered, "Wait a minute… They had an earthquake in Cardiff a couple of years ago, was that you?"

The Doctor frowned, "Bit of trouble with a Slitheen," he said, avoiding actually looking at either Martha or Reid as he continued in a slow sort of mumble, more to himself than to either of them. "A long time ago… Lifetimes. I was a different man back then."

He glanced toward the monitor on the console and pursed his lips, the tiniest traces of a frown on his face.

"What's a Slitheen?" Reid asked curiously.

"Oh, well… Big green aliens. 'Bout eight feet tall. Tried to start World War III and nuke the entire earth to sell it on the Black Market," the Doctor explained, still dancing around, fiddling with the controls.

"Black Market?" Martha frowned, "You're telling me there are people out there that would pay to have a destroyed planet?"

"Mhm, 'course there are," the Doctor said, as if that should have been entirely obvious. "Gotta run their ships with something. The Earth would make good fuel you know."

"So why not try to use another planet then? An empty one?" Reid frowned, "Why would they go after Earth instead?"

"Well back then you didn't have a whole lot of knowledge on aliens… Made you easy targets. Plus, they didn't even need to provide their own fire power. Just fake an alien invasion, get the nuclear launch codes from the UN, attack another country, they fight back and it's World War III, everyone dies and the Earth is radioactive chunks of fuel,"

"You're talking about what happened after that spaceship hit Big Ben," Reid said, frowning. "The news said that was just a hoax."

"Can't believe everything you read in the papers…" the Doctor said, "Anyway, saved the day, then when we came back to Cardiff ran into one of the Slitheens and, well, there was a bit of trouble, like I said, sent her home and that's the end of it."

"We?" Martha frowned, raising a brow.

The Doctor glanced at her, like he was trying to decipher that odd hitch in her voice, but was completely unable to. "Rose and Me, yeah, of course. Well, and a couple of others. Captain Jack and…" he paused, realizing it was a better idea to not mention Mickey, not after Martha had met him. He was still trying to figure out how the two of them had ever gotten married. It made no sense.

He skipped around to the other side of the controls, "Finito! All powered up," he said, glancing at the monitor again, his eyes going wide and then scrunching together, an odd combination of uneasiness and confusion.

"Are you okay?" Reid asked, taking a step forward. The Doctor just nodded and flipped another lever, grinning brightly as the TARDIS engines began whirring again. Reid thought he looked suspiciously relieved and started to ask him if he was really okay, but the TARDIS shook and a small explosion knocked them all over.

Reid ended up on his backside, head clanging against the metal floor, Martha slid back and forced herself up and the Doctor nearly stumbled into the console, grabbing hold as Reid struggled to sit up properly.

"What was that?" Martha asked, leaning over to look at the monitor, confusion and fear in her eyes despite her best efforts to calm her rapidly beating heart.

The Doctor didn't answer for a moment, putting his foot up on the console for balance as another small explosion sent smoke and sparks flying at them and Reid stumbled over to where they were, watching the monitor himself and wishing that he could read Gallifreyan.

"We're accelerating," the Doctor said, eyes wide with that strange combination of absolute perplexment and fear. "Into the future. The year one billion… Five billion. Five trillion… Fifty trillion? What?"

Reid and Martha stopped watching the monitor and started watching the Doctor's face, worry on their own faces. Whatever was happening had clearly never happened before and the Doctor had no idea what was going on. Around them the TARDIS was still shaking and they were all holding onto the console to keep from tumbling around the control room.

The Doctor was leaning close to the monitor, face scrunching up in disbelief, "The year one hundred trillion? That's impossible!"

"Why is that impossible?" Reid asked, watching his worried face.

"What happens then?" Martha asked, her eyes trained on him as well.

The Doctor glanced between the two of them, face still full of disbelief and confusion, "We're going to the end of the universe,"

~/.\~

The TARDIS slowly stopped shuddering and they released the console, Martha and Reid watching the Doctor anxiously as he looked around the slowly calming TARDIS. Their jolting, rollercoaster ride came to a gentle, if a bit bumpy, stop as the ship landed.

Martha met Reid's eyes and glanced at the Doctor, "Where are we? What's out there?"

The Doctor looked unsure, dark eyes looking around ominously, "I don't know,"

Reid looked surprised, "I never thought I'd hear you say that,"

For just a moment, the Doctor looked worried, eyes clouded and uncertain. "Not even the Time Lords came this far," he said, more to himself than to either of his companions. He took a breath and Martha and Reid waited, wondering if he was going to flip the controls and take off again.

"We should go," he said slowly, the words sounding so very foreign coming out of the Doctor's mouth. "We should… really, go."

Reid raised a brow, not believing the Doctor was actually going to leave such an opportunity behind. An unexplored world, hundreds of questions unanswered, just buzzing around in his mind and the Doctor was going to abandon ship? Not the Doctor he'd met, that was for sure.

And suddenly, the Doctor's face broke out into a huge grin, his dark eyes lighting with all the excitement of a child and he hurried toward the doors, grabbing his coat. Reid smiled and he and Martha followed closely behind him, each just as excited and curious as the Doctor to see what awaited them in this unknown and unexplored world.

It was dark out, no sign of a sun and only a very few remaining stars speckling a pitch black sky. It looked to Reid like they'd landed in some desolate waste land, no sign of life ahead for miles at least. He turned to the Doctor, about to ask him if anything looked familiar when Martha gasped and raced towards what he'd first mistaken as a rather large rock.

"Oh my God!"

Martha was kneeling beside the man, turning him over and pressing her fingers against his neck for a pulse, shaking her head, "I can't get a pulse… Hang on, you've got the medical kit thing!" She was on her feet again, racing back into the TARDIS for the kit. The Doctor moved toward the body, a sad look on his face, "Hello again," he whispered, shaking his head and stepping closer, wincing.

Reid finally got a good look at the man's face, his own gasp of surprise startling the Doctor.

"Jack!"

The Doctor turned to frown at Reid, "You know him?"

Before Reid could answer, biting his lip to keep from saying "Of course!", Martha burst back out of the TARDIS with the kit, trained fingers working nimbly as she approached, pushing a stunned Doctor and silent Reid away.

"Get out of the way!" she snapped, kneeling down, pulling out the stethoscope and leaning over to listen for a heartbeat, breath, any sign of life at all.

"Don't bother," Reid stopped her before she could really do anything, "Just… step back,"

Martha frowned, brows scrunching together as she looked up at Reid, "What are you talking about? What's wrong with you two?" She frowned, crossing her arms and staring up at the two immobile men in front of her. She'd have thought they'd be just the least bit concerned about a dead man lying just a few feet from the TARDIS.

Reid glanced at the Doctor, chewing his lower lip, "There isn't anything you can do," he said. "Right, Doctor?"

Martha frowned, "What d'ya mean? Do you know him?"

The Doctor nodded, "Used to travel with him, in the old days…"

Martha blinked, lowering the stethoscope, frowning, "But… he… How…?"

"How did he get here?" Reid asked, "I thought he was in Cardiff…I mean," he frowned, again swallowing his words. He wasn't sure how much the Doctor knew at this point; he certainly didn't want to say anything that could create a paradox of any kind. He was beginning to understand how difficult this must've been for "future" Martha.

The Doctor eyed Reid with a small, thoughtful frown, calculating that information and tucking it away for later examination. "Must've clung to the outside of the TARDIS, road with us through the Time Vortex… That's very him," he said, a surprised smirk on his face as he gazed down at the prone body.

Martha was still confused, a sad look on her face as she glanced back at Jack, "I'm sorry, but he's dead. I can't get a heartbeat, just… nothing."

Almost as soon as the words left her mouth the apparently dead body suddenly jerked, a loud, pained gasp escaping his lips as he lurched forward, eyes opening wide. Martha screamed as his flailing hands grabbed onto her arms and she turned to stare, wide eyed at the man.

"Well so much for me! Don't worry, I've got you," she tried to comfort him, every nerve in her body shaking as the man gasped for breath. Reid and the Doctor watched in relative silence, neither seeming to be too surprised at the sudden resurrection of their friend.

After a moment, he seemed to calm down and he met Martha's eyes, smiling a bit, "Captain Jack Harkness," he said, grin growing more confident as one of his previously shaking hands reached up to brush her cheek. "And who are you?"

Martha couldn't help blushing a bit, looking down as she smiled, "Martha Jones,"

"Nice to meet you, Martha Jones,"

"Oh don't start!" the Doctor snapped rolling his eyes. Reid couldn't stop the grin that spread across his lips at the sight of Jack flirting. It was so good to see the man, even if he hadn't actually met Reid yet.

"I was only saying hello!" Jack snapped, giving the Doctor an annoyed glare as Martha helped him to his feet, still blushing a bit. He grunted and grimaced as he stretched his tight muscles, breathing a brief sigh of relief before spotting Reid and straightening up, another cocky smile twisting his lips as he eyed the young agent up and down.

"…Whoa," he said, "Doctor, I knew you liked the pretty girls, but pretty boys?"

Reid felt his face heating a bit, thinking about Morgan for an odd moment. "Spencer Reid," he said, a tiny smile on his face.

Jack's eyes were bright, "Very nice to meet you, Spencer," he said, starting to holding his hand for Reid to shake. The Doctor immediately intervened, pushing Jack's arm away and frowning at him.

"Hands off,"

Jack somehow managed to both glare at the Doctor and smirk at the same time, "Why, is he you yours?"

They stared at each other in silence for a moment before Jack's face went a bit rigid and his eyes a bit cold, "Doctor," he nodded slowly.

"Captain,"

"Good to see you,"

"You too, same as ever… Although… Have you have a bit of work done?" The cold, tension in the air disappear somewhat and the two men visibly relaxed by a fraction.

"You could talk!" Jack said, motioning to the Doctor's entire body with an incredulous look on his face.

"Hm? Oh, the face! Regeneration. How'd you even know it was me?"

Jack smirked shaking his head, "Well, the police box kind of gives it away," he said, "I've been following you… Looked for you everywhere."

He paused, eyes going cold again, his next words partly snarled as Reid and Martha listened in apprehensive silence.

"You abandoned me,"

The Doctor chose not to react, face blank as ever. "Did I? Busy life. Moving on,"

Jack swallowed roughly, seeming to take the answer in and realizing it was probably the best answer he'd be getting from the Doctor anytime soon. "…I have to ask… Canary Wharf. I saw the list of the dead. Rose… is she…?"

"Oh, no, sorry! She's alive!"

Jack breathed a sigh of relief, "You're kidding!"

The Doctor was grinning now, but there was something sad in his eyes. Reid looked away, suddenly feeling like he was intruding on something private. Martha looked vaguely annoyed. Apparently they couldn't meet anyone from the Doctor's past with it brining up Rose again. What was so special about her anyway?

"Parallel world, safe and sound," the Doctor said, "And Mickey. And her mother."

Jack was slowly grinning, that cold tension almost entirely gone now. "Oh, thank God!" he rushed forward and hugged the Doctor, happier than he could really describe. Reid smiled a bit, shaking his head. He'd heard a lot about Rose Tyler from "future" Martha and Jack when they'd met. He wished he'd gotten the chance to meet her. She was apparently someone incredibly special, though the Doctor hardly ever mentioned her.

Martha looked dejected, sighing and shaking her head, "Good ole Rose," she muttered bitterly. Reid edged closer to her and smiled softly, putting a hand on her shoulder. She met his eyes for a moment and smiled back, glad there was at least one person there who wasn't fixated on the Doctor's old flame.

~/.\~

"So," Jack said, turning to glance at Reid, "How did you two meet?"

They were walking down a dark path, shrubs and brush the only signs of any life in the godforsaken landscape. There weren't even bugs. The Doctor was walking a few feet ahead of them, listening to the conversation and injecting his own input every so often. Martha had already told her story about meeting the Doctor on the moon, the Judoon and the Plasmovore with her bendy straw. Now it was apparently Reid's turn.

"Oh," Reid frowned, looking over at the Doctor and biting his lip, "Well, that's a little bit complicated. I met this regeneration a couple of days ago… Martha and the Doctor showed up claiming to be consultants on a case."

"Case?"

"He's an FBI agent," Martha said, smiling slightly.

Jack's eyes got that interested sparkle, "Hm, that explains the holster… Thought it was just a really sexy accessory,"

Reid blushed again and the Doctor gave Jack a harsh look, "Jack, stop it."

Jack sighed, "What? I can't make conversation?"

The Doctor just glared at him and Jack sighed, shaking his head and turning his attention back to Reid. "So he and Martha helped solve the case and he offered you a trip?"

Reid smiled, nodding. "Basically," he said, "But… well, it was… a lot more complicated than that,"

Martha snorted, "You can say that again… Never thought I'd see future me, even traveling with the Doctor,"

"You met yourself?" Jack sounded vaguely jealous as he glanced over at her, "What was she like?"

Martha shrugged, "Dunno," she said honestly, "I didn't really get to talk with her much. Really liked my hair that way though," she reached up to touch her hair, a thoughtful frown on her face, "I wonder what made me decide to change it…"

Jack smiled, "You met yourself and the thing you focused on was the hair?"

Martha smacked him playfully, "No! But it's not like I had a chance to talk to her… me," she shook her head, sighing, "There was a lot going on. We were fighting an alien serial killer, getting kidnapped and shot at and the Doctor wasn't helping matters. He was in a foul mood the entire time."

She rolled her eyes and shot the Doctor a pointed look, which he promptly ignored. "And then there were his headaches," she motioned toward Reid, "That was really interesting."

"Headaches?"

Reid nodded, "I… I'd been having headaches for a few months and they were getting worse," he explained, "The Doctor figured it was someone putting a block on my mind and he tried to undo it…"

He trailed off and glanced to the Doctor, who seemed to be doing his best to ignore the conversation at hand. "And when he did all these memories started coming back," he said slowly, "Memories of the Doctor and Martha. I, well, I'm not sure exactly what happened, but somehow the Doctor accidently crossed his own Time Stream and… things happened and then t- someone tried to erase my memory of it happening, which caused my headaches."

Jack frowned, looking thoughtful, "So you've met him before then? Just… in his future?"

Reid nodded, "A future regeneration," he said, briefly looking away, "You were there too."

"I was?" Jack's interest peaked and he grinned, "I don't suppose you could tell me anything, could you?"

"No!" The Doctor interrupted, frowning at them, "Absolutely not! We can't risk it." He glanced to Reid and there was a pained look on his face that clearly said he desperately wanted to risk it and hated not knowing when the answer was right in front of him. But he stoically reminded himself of the dangers involved in foreknowledge and trudged on, shaking his head.

Jack frowned, but shrugged it off and they followed after the Doctor.

"So, what about you, Jack?" Martha asked curiously, "You said he abandoned you. What happened?"

~/.\~

Jack had Reid and Martha enraptured with a tale of murderous game shows and a deadly battle with Daleks as they continued down the – still entirely void – path in the dark. The Doctor only speaking every now and then to correct Jack whenever he got a fact wrong.

He was, not surprisingly, tense when Martha demanded to know why he'd abandoned Jack. Reid, personally, would've liked to know that answer as well. The Jack he'd met hadn't mentioned the Doctor abandoning him and apparently there were no hard feelings about it, but he'd still like to know. It came as no surprise to him, the fact that the Doctor had left many companions behind. He'd seen the Doctor's life for himself, he entirely understood the nature of a relationship with the Time Lord and how dangerous it could be.

"Oh she was blonde!" Martha muttered sarcastically at a comment from Jack, shaking her head, "What a surprise!"

The Doctor, apparently having heard enough of their banter on the subject, turned around frowning, "You two look around you! We're at the end of the universe! Right at the end of knowledge itself and you're busy… blogging! At least Spencer has some sense to be interested in his surroundings rather than my past!"

Martha and Jack fell silent, realizing they'd hit a nerve and Reid bit his lip, jogging to catch up with the Doctor as he turned and walked off in a new direction, toward the edge of what Reid thought was a cliff.

"You shouldn't be too hard on them," he said quietly, "It's not their fault."

The Doctor was stiff, nodding, "I know,"

Reid rolled his eyes, "It's not your fault either, Doctor,"

The Doctor smiled a bit, "Just how well did you get to know the future me anyway?" he asked, turning to glance at him.

Reid sighed, shaking his head, "Well enough," he said, "Apparently your mood swings are nothing new."

"Oi!" The Doctor frowned, "I don't have mood swings!"

Jack snorted as he and Martha rejoined them, "Says who?"

"Wow!" Martha cut the Doctor off before he could answer, staring over the edge of the cliff and down into the cavern bellow. What looked like a market or a city had been carved into the rock face, buildings and stairways dotting the vast space.

Reid's hazel eyes shone brightly as he looked over the edge, "Is that a city?"

The Doctor looked thoughtful, "A city or a township or a conglomeration… It's empty now. Must've died out years ago." He looked up at the near pitch sky, pointing up, "Look at the sky; that's not just night. All the stars have burned out. Fading away into nothing."

"They must have some sort of atmosphere shell," Jack said, looking around the barren city, "We should be frozen to death by now,"

"Well," the Doctor glanced at the former Time Agent, "Martha, Spencer and me, maybe. Not so sure about you, Jack,"

Jack glanced at the Doctor and frowned, looking away quickly as Reid leaned forward and toward the edge, "What about the people? Do you think anyone survived?"

"They can't all have died, can they?" Martha asked, "Not if they've built that atmosphere shell thing."

The Doctor looked a bit skeptical, "Well, I suppose…" he looked at Martha's eyes and couldn't bear to say what he really thought: that finding life this far into the future, in a place this void and obviously nearing collapse, seemed impossible. "We have to think life will find a way. Somehow."

"He's not looking too bad," Jack said, a faint smile on his face he looked down into the deep bowl of the deserted area, pointing to a lone man, running at full speed over the rocky terrain. For one brief second the four of them smiled, thrilled to see that they weren't, as they all suspected, the only living things on this near dead planet. But then they spotted the rough, angry looking group chasing after the man, carrying what looked like weapons and torches in their hands as they ran.

The Doctor frowned, "Is it me or does that look like a hunt?"

~DW/CM~

A/N: So there it is. The first (fairly lengthy) chapter of "Armageddon". I hope you guys are enjoying it so far! Nervous about Jack, first time ever writing him! Hope he was in-character.

And for clarification, this story will be broken into five parts, as follows:

Part I: Utopia

Part II: The Sound of Drums

Part III: The Year of Hell

Part IV: Last of the Time Lords

Part V: The Kids Are Alright

Parts I and II will be brief, only a few chapters each (I'm aiming for about three each), Part III will be the meat of the story, not sure how long it'll be, but it'll be lengthy. Part IV will be the conclusion, probably two or three chapters in length. Part V will be short as well, though I'm not sure exactly how many chapters I plan for it. It'll be an epilogue sort of thing.

Anyway, I hope you enjoyed the first chapter! Please review!