Title: Armageddon

Rating: T

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

A/N: Thanks so much to all of the amazing reviewers! You guys are awesome and I really appreciate your support and comments!

So, I've decided that yes, Supernatural will be part of this crossover. Unfortunately, no John seeing as this takes place in 2007 and John was gone then. And no Cas either, unfortunately. Sam, Dean, Ellen, Jo, Bobby, Ash. For Supernatural it'll be in late season 2 (obviously before "All Hell Breaks Loose") around the time Dean tells Sam that John warned him about Sam's destiny (not that it's entirely relevant except that you know who's still alive and who's not.)

Anyway, hope you enjoy the chapter! Please let me know what you think!

Armageddon:

Part II: The Sound of Drums

Chapter Three

Reid watched curiously as the Doctor pulled out four keys that belonged to the TARDIS and slipped a string through them. He'd already had them start taking apart the laptop and welding things onto the keys for whatever his plan was, which, at the moment, Reid only vaguely followed.

"What are the keys for?"

"Four TARDIS keys," The Doctor explained, "Four parts of the TARDIS, all with low-level perception power because the TARDIS is designed to blend in. …Well, sort of."

Reid raised a brow, lifting one of the keys, "The keys themselves can alter perceptions?"

"Mildly. Not powerful enough for what we need," The Doctor said, "But, now, this Archangel network has its own low-level perception signal. So, weld the key to the network and… Martha? Look at me, you can see me, yes?"

"Yep, of course," Martha nodded while Reid and Jack turned and watched curiously. Reid was pretty sure he was following him now. He didn't know exactly how perception filters worked (he'd love to have a chance to really study that) but he figured the keys were supposed behave like some sort of… sheild to be hide them from the Master and the police.

The Doctor held up one of the keys on a string and looped it over his neck, "What about now?"

Reid blinked and frowned, squinting his eyes and noticed Martha doing the same. He tried to focus on the Doctor, but it was like he couldn't quite get his eyes to shift to where he was standing. He knew he was standing there, but he was sort of an afterthought, out of focus.

Jack chuckled, shaking his head in amusement, knowing exactly what was happening with the perception filter having used the one in Cardiff frequently with Torchwood.

"I'm here," the Doctor said, wiggling his fingers. "Look at me."

"It's like… I know you're there," Martha said, frowning, "But I don't wanna know."

The Doctor grinned, slipping the key from around his neck, "And back again!" he said, going back over to the other keys. "See? It just shifts your perception a tiny bit. Doesn't make us invisible, just unnoticed."

He paused, trying to think of a way to explain it. Then he smiled and turned Martha excited, "Oh! I know what it's like! It's like when you fancy someone and they don't even know you exist. That's what it's like! Come on!"

Reid pressed his lips together and Jack signed shaking his head sadly, "You too, huh?" he said, giving her a look so pitying it made her want to scream as he followed after the Doctor. Martha sighed and shook her head.

"If it means anything," Reid said quietly, "I don't think he actually doesn't notice you…"

Martha snorted, "Could've fooled me,"

"It's that he doesn't want to,"

"Thanks, Spencer, I feel so much better now,"

Reid smiled a bit, "No, that's not how I meant it… I just… I think he's scared to hurt you. It hasn't really been that long since he lost Rose, I don't think, and he blames himself for that. It's not you, it's just him."

Martha smiled and shook her head, "Well, at least one of us has the sense not to fall over him like some love-sick teenager," she said.

Reid looked away and nodded, "Yeah…" he said slowly, sounding just a bit uncertain and clearing his throat. "Come on, we should, uh, catch up with them."

~/.\~

Mycroft frowned down at the file for the Jones girl and her partners. Names hadn't been given for two of the men and the third one was apparently Spencer Reid, a young FBI agent. Who was still in the United States and couldn't have possibly been anywhere near Martha Jones or her family, he'd checked.

He'd looked into the Jones family as well, discreetly, of course. And found nothing of consequence. They were a normal, boring family with their own normal, boring problems. Martha was a medical student, Tish was a PR worker for Saxon, Leo was working at a garage at the moment, but taking classes to get a better job, the parents were divorced, father a construction worker, mother didn't work. They were not the usual terrorists that he dealt with by any stretch of the imagination.

One of the unnamed partners of the still-at-large Miss Jones had been identified as Jack Harkness. A name Mycroft knew well, though he'd never personally met the man. Leader of the "clandestine" Torchwood. The name had been cropping up more and more lately, he'd been handling complaints from Scotland Yard about Torchwood taking over cases and interfering in their business. Officially, Torchwood didn't even exist, but digging through miles of red tape one could find that they were a sort of government agency that only handled special cases.

What "special" meant wasn't mentioned, but Mycroft knew that too. Alien hunters.

He'd known about Torchwood since before Canary Wharf, though back then what they did wasn't exactly clear to even him. Then came the ghosts and Cybermen and those metal flying things and Torchwood was gone for a long time before it came back with an entirely new attitude. Still trying to hide in the shadows, but coming out more and more.

Harkness was an interesting case because the more Mycroft found out, the less he really knew. The other man was still unidentified, but he'd put calls through to contacts in every government agency he could while avoiding the attention of Saxon. He still didn't trust the man and the President was arriving in just a few short hours so he'd have to be as prepared as possible to deal with the political mess that was descending.

First things first, however, he wanted to know exactly what happened with the Jones family. Unfortunately, that would require quite a bit more legwork than he was willing to do.

"Brother dear," his younger brother's voice was a sarcastic sneer over the phone. "Surprised you had time to call, with all the fires you've no doubt been putting out lately thanks to our new Prime Minister."

"I don't have time for this, Sherlock," Mycroft sighed, "I have something I need you to look into. I assume you've heard about the Jones family?"

"Of course," Sherlock scoffed, "And that ridiculous story about them being terrorists. I hope that wasn't your idea, Mycroft, it's really quite beneath your intelligence."

"Not mine. Saxon's," Mycroft said. "Whatever happened with that family, Saxon's keeping it hidden."

"So hidden even the great Mycroft Holmes can't find the truth on his own?"

"Sherlock!" Mycroft pinched the bridge of his nose, "There is something very wrong here and it's only just beginning. I need you to find out what really happened with the Joneses."

"Why should I?"

"We are talking about the fate of the entire United Kingdom, little brother," Mycroft said tersely.

"Oh, don't be so dramatic, Mycroft," Sherlock said, "You know I could care less about your political games."

Mycroft sighed and lifted the photograph of Jack, studying it, "It involves Torchwood," he said quietly.

"What? How?" Now Sherlock was interested.

"Captain Jack Harkness is among the fugitives with Miss Martha Jones,"

"…I'll look into it,"

~/.\~

Prentiss perched on the edge of her desk, Morgan, JJ, Garcia and Reid all gathered around her as well. Hotch and Gideon were standing behind her. All around the BAU, paperwork had been left undone as agents stood around, watching the television that was tuned in the news.

Air Force One was about to land in London to meet with Prime Minister Harold Saxon.

"I can't believe he thought he could just flaunt contact with aliens and not have UNIT get involved," JJ said, shaking her head.

"I can't believe people believe he's telling the truth," Morgan said, "C'mon, aliens? Really?"

"How can you still be skeptical about extraterrestrial life forms?" Reid asked, "After what happened last year?"

Morgan made a face, shaking his head, "I'm sure half that stuff can explained as mass hysteria and pranks gone really bad."

"What about the stuff that can't be explained?" JJ demanded, "Not everything is so black and white these days. Weird things have been happening more and more often."

Morgan nodded, "Okay, fine, so maybe there is something out there we can't explain. Doesn't make it aliens, and even if it is, this guy was just elected and all of a sudden he's contacted by floating metal aliens? No, this is either fake or the guy's a nut-job."

"Oh, c'mon, have a little faith, Derek!" Garcia grinned, "This could be like a Sci-Fi movie! What if the aliens are evil and try to steal all the women and children?" her eyes sparkled as she teased him and Morgan laughed.

"You wouldn't have anything to worry about, Baby Girl," he said, "I'd be here to protect you."

"Shh," Prentiss suddenly straightened up, "They landed!"

~/.\~

It was dark and a bit cold as Martha, Jack, Reid and the Doctor managed to sneak their way into the huge and vacated airport where the Master was meeting with the President. Reid felt a bit uneasy, standing there, watching President Winters talk with Saxon. UNIT had just taken total control over the entire operation and the meeting with the Toclafane was to take place on board the UNIT ship, Valiant.

Reid was surprised at how little the Master seemed to be bothered by America's butting in. He seemed more concerned about whether or not the event would still be televised.

"Since it's too late to pull out now and since Britain elected an ass, yes, the world will be watching," Winters said, glaring at Saxon furiously. "Me."

Saxon grinned and watched the President and his men go back to their SUVs and drive off. He took Lucy's hand and leaned in close, "The last president of America," he said cheerfully. As everyone cleared away, the Master turned and stared toward where they were standing, squinting his eyes suspiciously for a moment.

Reid swallowed roughly and felt Martha's hand grip his tightly again, until Saxon turned away and a Police van pulled up.

The Master grinned and began jumping around excitedly as Martha's parents and sister were pulled out of the van and herded away. He was laughing and taunting them like a child, eyes shining with joy.

"Don't move," the Doctor hissed quietly to Martha, sensing her urge to rush at her family.

"But –"

"Don't," he said, "Not now."

"I'm gonna kill him," Martha whispered, her throat tight as she stared at her family. The only good thing she'd seen was that there was still no sign of Leo. At least for now her brother was still safe.

"I say we use these perception filters to sneak up on him and snap his neck," Jack said quietly.

The Doctor turned to Jack, giving him an odd look. "Now that sounds like Torchwood," he said.

Jack flinched a bit, but didn't look away. "Still a good plan,"

Reid couldn't help but agree. Everything the Master had done, all the people he'd hurt, he would just continue to hurt more people, kill more people, if they didn't stop him.

"He's a Time Lord," the Doctor said, "That makes him my responsibility. I'm not here to kill him, I'm here to save him."

Reid felt a pit in his stomach at those words, but shook it off and cleared his throat, "The Valiant," he said quietly, "That's where they're going, right?"

Jack nodded, pushing buttons on his Vortex Manipulator, "Yeah, it's a UNIT ship. I've got the coordinates here."

"Does that thing work as a teleport?" the Doctor asked, glancing at it curiously.

"Since you re-vamped it, yeah,"

"Good. That's how we get on board."

Jack nodded seriously and the three of them gripped Jack's wrist as he set the coordinates and they vanished in the blink of an eye.

~/.\~

"Up there!" Ianto was the first to spot the building despite Owen's sharp eyes scanning every inch of the wasteland. It had started snowing about ten minutes ago and they were all hugging themselves to keep warm. The sight of the building brought relief to all of them as they quickened their pace, reaching the building in just a few minutes.

It was what looked like an old research center and the power was still going as they entered, lights on, heating, everything.

"I thought this place was abandoned, Tosh?" Gwen frowned, turning to glance at the other woman.

"It is," Tosh said, "Or was, at least. It used to be an old research post but they shut it down years ago. It hasn't been used since then except by Torchwood One, back in the old days. They haven't even been out here since before Canary Wharf."

"Great," Owen sighed, "So either there's someone else here or we are screwed."

Ianto was frowning, standing father inside the building than the rest of them, holding his gun in his hands. It still didn't seem quite right there, the heavy weight on his palm making him nervous as it usually did. "Guys," he called over his shoulder, "I think there's someone in here. I can hear a voice ahead…"

Gwen took a deep breath, "Alright. Ianto, Tosh get behind me and Owen. Stay together. We don't know what's going on yet,"

They eased their way down the dim-lit hall and could definitely hear a male voice speaking from within, though they couldn't figure out who he was talking to. Gwen held up her gun and mouthed instructions to the others before jerking forward and aiming her gun into the room.

The empty room.

There was no one inside at all and the four of them slowly lowered their weapons.

"What the fuck?" Owen frowned, looking around. They could still hear the voice, muffled so they couldn't quite make out the words.

"Over here!" Ianto nodded toward the far corner of the dark room where a television was glowing softly and on the screen was none other than Harold Saxon.

"The Prime Minister?" Tosh frowned, "What?"

Gwen knelt next to the TV and turned the volume up to hear whatever he was saying.

"-lo, Torchwood! Congratulations! You've done exactly what I knew you would. Isn't it lovely when stupid little pawns play their parts perfectly?"

"What the hell is he talking about?" Owen frowned, squeezing his gun tighter as he stared around the dark room.

"You're probably a bit confused by now and no doubt freezing. The Himalayas is so beautiful this time of year, aren't they? And lucky you! That gets to be the last place you'll ever visit on planet earth!"

"We should leave," Gwen said, the others nodding in agreement and turning toward the door only the find it suddenly slam shut in their faces. "What the -?"

"It's locked!" Tosh said, tugging hard on the handle. "It won't budge."

"Wonderful," Owen muttered, "We're screwed."

"It's a pity. You all seem like such interesting playthings, but I can't have you messing around with my plans for World Domination, now can I? So, have fun with your little friend. Maybe it'll even be quick, but how boring would that be?"

The recording stopped, skipped for a moment and then began replaying, "Hello, Torchwood! Congratulations! You've done exact-"

It didn't get to finish because Owen shot the television screen and it fizzled out of life, leaving them standing completely in the dark.

"Torches," Gwen snapped, pulling her light from her pack while the others followed suit. "As long as we're stuck here, we might as well figure out why."

"You heard him," Owen said, "Britain's got a fruit loop as Prime Minister,"

"Or a new Hitler," Ianto said, "Apparently."

"Just come on!" Gwen said, shining her light around the room. It was an old computer lab, apparently, but none of the computers looked even remotely functional.

"There's a door!" Tosh announced, "Over here! It's open!"

"Oh, thank God!" Gwen sighed in relief as they pushed the door open and entered another hall, "Maybe there's another way out of here…"

The floor sloped down as they continued walking and led them into what might have been a storage room at one point. Might have been, because that was certainly not what it was now.

"Is that a…"

"Can't be,"

"It is," Ianto's voice shook a bit. "That's a Cyber-conversion Unit."

"Complete with Cyberman," Owen muttered darkly, shining his light onto the metal man currently strapped down in front of them. "Said it before, we're screwed."

~/.\~

They landed on the Valiant and stumbled, nearly falling down.

"My God that's rough!" Martha winced, shaking her head to clear the pain.

"I've had worse nights," Jack said, cracking his back and blinking a few times. It took them a few minutes to get the feeling of the teleport to wear off, but then they were heading down the dark hall. It was dawn already, the early more sun like a horrible omen to Reid.

They had less than an hour before this ended. He took a breath and hurried to catch up, hearing an odd, horrible noise as he did.

"The TARDIS!" The Doctor's eyes nearly bugged out his head as he stared at her, thrilled to see his ship again.

"What's it doing on board?" Jack frowned as the Doctor rushed to her and threw the doors open, stopping dead as he looked inside.

"Don't touch it!" he warned Jack as the others stepped in after him.

"Wasn't going to," Jack assured him, "…But… what is it?"

"That sound," Reid frowned, "It's awful,"

Martha nodded, "Sounds like she's sick," she said, "What is this, Doctor, what happened?"

The Doctor's eyes were wide with pain and horror as he stared at the TARDIS and the horrible red lights, feeling the pain she felt and hating himself for it. "He's cannibalized the TARDIS," he said grimly.

Jack was studying it with an anxious look on his face, "Is this what I think it is?"

"It's a Paradox Machine," the Doctor's voice had gone dark and angry and the three of them watched cautiously. They all knew well enough how he felt about the TARDIS and couldn't even imagine what he was going through right now, staring at this horror being inflicted on her. He swallowed roughly, shaking his head.

"We'll fix this," he promised. "We don't have much time. Let's go."

~/.\~

"Dude, can you believe this?" Dean was sitting on his bed in the motel, lacing up his boot. The television was on, tuned to the news for a change, though that was Sam's doing and not his. He wanted to keep up with any updates they might have on the Winchester brother fugitives. Lately, news about the armed robbery had died down and they hadn't seen Dean's photo on the news in several days.

Sam stuck his head out of the bathroom, frowning, "Believe what?" he asked.

"Aliens," he said, "President flying in to meet 'em and everything. It's crazy."

Sam smiled, "Aliens are crazy? Dean, where were you last year?"

"Come on, Sammy, don't tell me you actually believe that was aliens? There's no way."

"Then what?"

"Demons," Dean said, "I dunno. Demons like we've never seen before. That Yellow Eyed son of a bitch has been planning a war, remember? Maybe longer than we even realized. Maybe they're demons we haven't seen before."

"Demons that wear metal suits?"

"They were converting people, Sam, remember? That's demon MO,"

"Whatever," Sam shrugged, "Aliens or demons doesn't really matter. Apparently the ones Saxon met are safe enough,"

"Yeah. And creepy. Didn't you hear that voice? It was like a kid or something. Dude, what if they're like possessed metal balls or some spirit is controlling them or something?"

"Crazier things have happened," Sam conceded, tugging his boots on as well.

"Exactly. Ask me," Dean said, "I say the President and that Prime Minister don't know what the hell they're screwing with, but it's probably bad news. Always is, right? Casper the friendly ghost just doesn't exist."

Sam rolled his eyes, "Right, well, I don't really care, Dean. We're here to do a job, remember? It's almost midnight."

"Yeah, yeah, I'm coming," Dean sighed, clicking off the TV and grabbing the keys to the Impala. "Let's go find us a dead guy,"

~/.\~

They stood in the back of the meeting room in the Valiant, listening to the President's speech. Reid was nervous, tense and watching the clock as the Doctor explained the plan. They would get the key around the Master's neck and people would see him for what he was. Of course, with everyone on Red Alert, that would be difficult.

He was tense as the Doctor began moving slowly, carefully as the clock struck 8 and the Toclafane appeared. Two minutes. Two minutes until the President died.

Saxon suddenly jumped up, announcing that he was The Master over the Toclafane and the Doctor stood frozen for a second when the Master gave the order to kill the president. "Oh God…" Martha gasped as he fell and the Doctor moved as quickly as he dared to get to the Master.

"Grab him!" The Master suddenly yelled the Doctor found himself held in tight hands. "Doctor! We meet at last! Ooh, I love saying that!" he grinned brightly. Reid, Martha and Jack reacted without thinking, running forward and Master reacted quickly, pointing a screwdriver at them, a bright light shooting out and hitting Jack square in the chest, where he fell. Dead.

"Laser screwdriver," The Master grinned, "Who'd have sonic?"

Martha and Reid knelt by Jack's body, gripping his hands as people around them panicked.

"And the best part is, he's not dead for long! I get to kill him again!" the Master grinned brightly, laughing excitedly.

"Master, just stop! If you could see yourself, please –"

The Master grinned brightly down at him before addressing the TV crews that were still filming for God knows why. "Excuse us, personal business. Be a moment. Let him go!"

The Doctor was thrown down to the ground roughly and Martha and Reid watched in horror, flinching as he shoved himself up and stared up at his adversary desperately, "Master, please, just listen to me. It's the noise in your head, the drums! I can help you, you can stop this!"

"Oh, how to shut him up?" he mused, mocking him before kneeling down to his level, "Oh I know!" he grinned brightly as he snatched the Doctor's head up and twirled the screwdriver idly in his hands, eyes dancing as he dangled it under the Doctor's chin and suddenly gripped his temple harshly.

The Doctor screamed, his mind assaulted with a thousand different, horrible images and sounds before the Master shoved him away and switched something on the screwdriver, a red laser shooting out this time and hitting the Doctor.

"Doctor!" Reid was the first to reach his side when the Master's attack stopped and the Doctor lay on the ground, panting and gasping, hardly able to breath. Martha was right behind him though Jack was still recovering from his previous death.

"Oh, she's a would-be Doctor!" The Master grinned, "And the Doctors newest little pet…" his eyes sparkled and Reid forced himself not to look up at the man. "But tonight, we've flown them in all the way from prison, just for you, Martha Jones, YOUR FAMILY!"

The Jones family was ushered in by the guards and the Master was grinning broadly as he watched her face turn to stone. He grinned triumphantly and turned to the people and cameras, addressing them as the new Lord and Master as the sky above them cracked and millions, or perhaps even billions, of Toclafane descended from the sky.

The Doctor grabbed Martha and pulled her down, whispering something Reid didn't quite catch as he held the Doctor's hand, unable to look away from the sight of the sky darkening with those things. This was wrong. This was not what had happened at all. This ended almost as soon as the president died. What was going on?

"Remove one tenth of the population!"

The Master's voice rang out loudly over the speakers and the Toclafane began flying dizzyingly fast, black blurs in the dark sky, to obey their Master.

Martha nodded, swallowing tears and moving back to Jack, not realizing that Reid wasn't with her at first. She took Jack's Vortex Manipulator and he gripped her hand tightly, "Get Reid and go," he said, "Hurry."

She stood, her legs feeling like jelly, and moved toward Spencer to grab him and get out of there, but as the speakers of the Valiant began playing "Voodoo Child" loudly and Lucy Saxon began to dance giddily with her husband, the Master saw her.

"Stop her!"

Reid wasn't looking at first and was too far away for her to teleport with him. She swallowed roughly and looked back to Jack, who yelled "GO!" and she looked toward her family, chained and terrified. Tears were trailing down her face as she pressed the button with shaky hands and was gone in the blink of an eye.

The Master didn't look altogether too worried to have lost Martha, he was certain he could get her back easily. She was no threat and he wasn't going to let anything ruin this moment for him. He spun around and yanked the Doctor to his feet as guards grabbed Reid and Jack and pulled them toward the Jones family.

"And so it came to pass that the human race fell. And the earth was no more," the Master said, his hand resting on the Doctor's shoulder as he supported his still weakened body and forced him to look out the window and down to the horror that was the earth bellow.

"And I looked down upon my new dominion as master of all. And I thought it good."

~DW/CM~

A/N: And this ends "The Sound of Drums"! Coming soon: "The Year of Hell"! This ought to be fun.

And yes, I know, the Master actually aged the Doctor in the end, but I hated that so I changed it. Not really gonna have an effect on the outcome, torture is just so much more appealing, you know?

Anyway. Hope you enjoyed! The REAL fun is just beginning and I've got so many more characters to introduce! Please review!