Title: Armageddon

Rating: T

Warnings: Major spoilers for "Utopia", "The Sound of Drums" and "Last of the Time Lords"; violence; mild language; allusions to rape (but I promise nothing explicit or graphic)

A/N: I'm amazingly managing to keep this every Tues. or every other Tues. schedule. I would have posted this last Tuesday, but it was Christmas Eve and I didn't want to post then and I tried to have it ready Monday, but I was doing a lot of research so the chapter didn't get done until later. Sorry guys. Still, thanks so much for the reviews and favorites. I appreciate it!

As I said last chapter, this chapter contains some things that may be upsetting or triggering. The really touchy thing: Miscarriage. Tread lightly here guys. There's nothing terribly graphic, but it's still really awful.

Now, onwards to the chapter.

Please don't forget to review!

Armageddon:

Part III: The Year of Hell

Chapter Thirty-Five

The common room in Rufus's bunker was buzzing with raised voices and rustling papers and excited chattering. Plans for their new weapon were already underway and they were still talking about Gabriel and the other so-called angels when suddenly six more people were just dropped into the room without warning. For an exaggerated moment all chattering stopped and they just stared at them and then the dam broke and everyone was talking at once.

Garcia cried out and nearly ran from her seat at the sight of Morgan, enveloping him in a hug tight enough to crush his spine. He was grinning from ear to ear and pressed a kiss to her hair, shaking his head at her.

"Alright, Baby Girl," he fought to step back, "you gotta let me breathe."

Garcia had tears in her eyes and shook her head, laughing and crying at the same time. "No, no, no, Derek, you don't understand. You're alive. You're alive and I thought you were dead and don't you ever, ever do that to me again!" She smacked him playfully and he nodded, hugging her tighter.

"I promise," he said. "I'll do my best."

Jane went right to Lisbon. His smile might've broken glass it was so bright. Lisbon's eyes lit up when she saw him as well and she went in for an awkward hug, stopping halfway. Jane didn't let her though, pulling her closer and holding her there until she hugged him back.

Stepping back, Lisbon cleared her throat and smiled at him crookedly. She didn't quite meet his eyes.

"I'm glad you're alright," she said, her voice a quiet rasp. Jane smiled at her widely, his eyes sparkling and then he yanked her in for another hug.

"I'm glad you're alright," he told her. If Lisbon hadn't known better she might've said his voice was choked up with some undefined emotion, but she chalked it up to relief and held on to him a second longer than she really needed to, glad to have him back.

Grace searched the group for Rigsby and when she spotted him her eyes lit up. Before she realized it, she was already across the room. She stopped a few feet from him, awkwardly smiling and Rigsby closed the distance, clearing his throat a bit.

He lifted his hand and then let it drop in some aborted attempt at a handshake or maybe a hug.

"…You're alive," he said, smiling at her.

She smiled back and nodded, reaching toward his hand and hesitantly wrapping their fingers together. "So are you,"

Ducking his head, Rigsby studied their intertwined hands and nodded, "Yeah…" His face was turning a faint pink color and Grace let go of his hands.

"I'm glad you're back," he said, clearing his throat. "I mean… glad you're not dead."

She laughed and nodded, "Me too," she said brightly.

Garth was making his way through pretty much everyone he had any real connection with, hugging them and grinning brightly at them as he did. Dean watched him with a dubious smile on his face, not sure how he could even be surprised at this point.

Looking around, Dean was amazed that so many people could even fit in the small space. There were even some people he'd only ever seen over a computer monitor before. The Master must have found the other safe houses as well, or was close to it. He wondered what made Rufus's bunker safer than the others, but he didn't get a chance to voice any of his questions.

Sam suddenly gripped him tightly by the arm, his fingers digging in almost painful. Dean scowled and turned to snap at him when he caught sight of Sam's face – pale and pinched like he always looked before something bad happened. He nodded his head forward and Dean turned to see Adam standing there, his eyes as big as saucers.

The talking lulled for a moment, chatter from the reunions dying down. Adam just stared at them for a long minute before he finally spoke. His voice was shaky and wrapped up with pain and confusion.

"They said that you were dead…"

Sam started to speak, but Rufus cut him off, his expression angry and suspicious.

"He was," he said. One hand rested on his shot gun as he eyed Sam up and down. All talking stopped then as the others realized that there was a dead man standing among them. Most of their attention was on Sam, but Rufus and Ash were staring at Dean suspiciously and Dean shifted on his feet awkwardly.

"It's a long story, alright?" he said defensively. "I couldn't let Sam die… I – not like that. I couldn't just watch him be dead."

"So you'd rather he was dead some other way?" Rufus demanded, "What? Starving to death when we run out of food and can't find more? Killed by the Master himself when he gets captured? Death's everywhere these days, boy."

Dean scowled and shook his head, "You don't get it," he said, struggling for words. He looked helplessly at Sam and fumbled, "I just – he's my brother. He's my family…"

Ash frowned, "What'd you do?" he asked. "Work some hoodoo spell? Try to summon another Reaper?"

Dean opened his mouth to answer, then closed it. Sam sighed and shook his head.

"He sold his soul,"

Rufus nearly slammed his gun down on the table and several others stared in shock and confusion at the news. Adam took a step forward and frowned, eyeing Dean.

"But before… with Amelia, you said that –"

"I know what I said," Dean snapped. "I changed my mind."

Sam snorted, "Dean's aware of the fact that he's a giant hypocrite. He doesn't care."

"Doesn't… but… he sold his soul!?" Juliet seemed to be having trouble grasping the concept.

Gus nodded, "I'm not an expert, but isn't your soul kind of important?"

"Apparently not," Sam snapped, giving Dean a look that could melt ice. Dean could feel his anger rolling off of him and he wished he could explain that he'd done it for him, to save him, but he knew Sam didn't see it that way. Sam saw him throwing his soul away for nothing and Dean wouldn't change his opinion. So he changed the subject.

"Enough about my soul," he said. "It's over. Sam's alive. Let's move on. What's happened since we've been gone?"

~/.\~

Gabriel, Castiel and Uriel didn't stick around when they zapped Dean, Morgan, Sam, Garth, Lisbon and Grace Van Pelt to the already overcrowded bunker in South Dakota. Uriel and Castiel immediately returned to their posts in Heaven, greeted by a smirking Balthazar, who assured them that they were safe from the prying eyes of Michael or Zachariah for the moment. Gabriel didn't pay attention to where he ended up; he just knew he was alone and thinking.

It was strange, seeing his brothers after so long. He barely knew Castiel, and Uriel and he had never been close either, but it he felt something tugging inside of him. If he were human he might have said his heart had lurched or something to that effect, but angels didn't really have hearts. Not that way, at least.

He'd told himself that he didn't miss Heaven. He didn't need those self-righteous ass-monkeys. They were dicks with wings, after all. But they were his family and now that he'd seen them – two of them at least – he missed them. He felt a sickening pang in his gut like homesickness that was difficult to shake. He couldn't go back and he knew if he did things wouldn't have changed.

Hell, from what Castiel and Uriel had said, things had gotten worse. Michael was sailing them right toward the edge of the real Armageddon. Part of him couldn't wait for that to happen. One big bang, one last giant hurrah and then it would finally be over. No more fighting, no more wars. No more wishing he could go home even though that was impossible. No more wondering where the hell their Father was or why he'd abandoned them. Nothing but endless peace.

Laughing, he wondered if it were a tiny bit twisted of him to save this planet from certain doom now, when he knew it was all going to go up in flames one way or another just as soon as the seals started breaking. And with Dean Winchester buying himself a one-way ticket to Hell, those seals were going to be breaking soon. He glanced skyward and wondered what Michael was going to tell the garrisons about that, how he was going justify himself to them when the real end began. He should probably care, but he didn't really want to.

~/.\~

It was swelteringly hot in the conference room. The Master's mood had not improved since he'd discovered the hideout in Oklahoma abandoned. The temperature in the room had been fluctuating between freezing and boiling for the past several days and none of the people onboard could catch a break.

Footage of David Rossi's body being tossed over the edge of the Valiant had been broadcasting on loop for the last forty-eight hours. The Doctor was certain that he was trying to goad the rebels into another foolish attack on the ship just to have another chance at capturing them.

He was also certain, from what he had been glimpsing over the Archangel network, that it would not work.

For the past few days he had been left to himself, sitting there and watching everything happen in front of him. He'd expected the Master to take his anger out on him and the other prisoners, but he hadn't come near him and the others hadn't left their cells since Rossi's death. He had a feeling it was the calm before the storm, however, and remained on his guard.

The Doctor was waiting, quietly working his way into the network farther, trying to take advantage of the Master's distracted anger. He knew something bad was coming, but he hadn't expected it to come in the form of a calmly smiling Lucy Saxon.

She entered the room alone and almost floated across the floor. She was barefoot for the first time in the Doctor's memory and her feet made no sound. She was smiling and humming and even though there was a dark bruise splotched across her pale cheek, her eyes were bright.

Lightly, she touched her hand to her forehead and pulled it away, studying the sweat that had collected there. Her voice was as airy as her smile as she looked up and met the Doctor's gaze.

"Harry's been in such a mood lately," she said, matter-of-factly.

"Isn't he always in a mood?" the Doctor was watching her with narrowed eyes. He'd never seen her like this before. She seemed to be in a different place, gliding along without a single care in the world. It was strange, to say the least.

Her smile twitched and she dipped her head, fingers brushing against the bruise. "I suppose," she said. Then her eyes lit up again and she smiled with all her teeth showing. "But he'll calm down," she said, "I've just found out the most glorious news. He'll calm down. He'll set the temperature right and he'll see to you and your friends getting a proper meal. I'm sure of it."

She moved around the room, still feather-light on her feet. She was so thin and the Doctor realized she was still wearing her dressing gown, the thin white fabric trailing around her knees. There were fading bruises on her arms and shoulders. Lucy didn't stop moving until she was standing in front of the great window where she had stood all those months ago with the Master, watching the Toclafane descend from the skies.

Reaching out, she put a hand to the glass, just where the sun was beginning to set, and pressed her forehead there. Her breath fogged the view and the Doctor sat up a bit straighter on his knees to see her better.

"Lucy?" he cleared his throat and frowned at her. She lifted her head slowly to look at him, smiling softly.

"What news?"

Blinking, Lucy leaned up again, her back straightening. Her brow furrowed for a moment and she cocked her head to the side, like she was trying to remember something. Then her face was light and bright and distant again and she wrapped her right arm around her middle protectively.

"I'm pregnant!" she said, nearly glowing with her happiness. "Isn't it wonderful?"

She didn't wait to hear the Doctor's thoughts and didn't seem to notice the look of horror on his face. She turned back toward the window and pressed herself against the glass, staring out at the sunset.

"It'll be so perfect," she said. "It'll be like it was before, now that we're having a child." Her arm tightened around her middle. "Harry will be happy again. I know he will…"

~/.\~

Tosh huddled with John, Jake and Sherlock as Ianto stood next to their modified metal detector. It had taken two months, but they and their allies in the USA were ready to test their first working weapons.

Ianto took a deep breath and flipped the switch, grinning when the air was filled with a faint, electric buzz. The metal seemed to vibrate with it and he stepped back, studying it. It was just an ordinary body scanner they'd found in an airport, but he felt a feeling of reverence watching it.

"How will we know that it works?" Jake asked, curiously frowning at the device.

"We'll come back and check in a couple of days," Tosh said. "We'll have to be careful; if it does work the Master could catch on quickly…"

"It doesn't matter how quickly he realizes," Sherlock said. "As soon as we confirm that this works, we'll be able to install several more of them. We will have made a significant dent in the Toclafane population."

"It certainly is looking up," John said, smiling. He glanced over to Jake as he'd been doing periodically since the nightmare that had nearly put Jake into a coma. Only, Jake wasn't standing next to Tosh where he had been seconds before.

"Jake?" John turned around, searching the area for him. "Where's Jake?"

"He was just here," Tosh was staring at the spot where Jake had been. "Just a moment ago. I swear…"

"He can't have gone far," Ianto said. "The area's flat. We'd see him…"

Sherlock had moved to where Jake had been standing before his mysterious disappearance. He sniffed the air and frowned, dropping to his knees to examine the ground. His fingers skimmed the concrete. Lifting his hand, he studied the yellowish substance that now coated his skin.

"Do you smell sulfur?" John suddenly asked, sniffing the air with a frown.

Sherlock looked up, the yellow dust still on his fingers. "I think we can assume that Jake did not disappear willingly…"

~/.\~

The machine flickered to life, buzzing loudly for a moment before the sound tapered off to a quiet hum. Prentiss's face lit up and she grinned, snatching Tony's hand in hers. She, Tony, Grace Van Pelt, Rigsby, Dean and Sam were together putting together one of the weapons they had built in the last two months. The others were broken into groups as well, installing the devices where they could in the larger cities surrounding the Master's weapon factory in South Dakota.

Tony held her hand tighter and then without warning, pulled her close and kissed her. Prentiss's grin widened and she pulled back, studying his face for a second before kissing him back, enjoying just that one, blissful moment of happiness.

Rigsby watched them for a second before turning away awkwardly and nearly stumbling into Grace. She smiled at him.

"Guess they're happy about the weapon working," she said.

"Yeah, guess so," Rigsby cleared his throat, rubbing the back of his neck nervously.

"It's nice, isn't it?" she asked, "that they can find someone to love even in this awfulness?"

His lips quirked a bit and he nodded, not entirely trusting his voice at the moment. He tried not to look at her or think about how pretty her smile was, reminding himself that they were still in a serious situation at the moment.

She smiled again and nudged him gently in the ribs.

Dean and Sam watched the exchange, Sam with a faint smile on his face and Dean with a sick look. Sam turned toward his brother and tilted his head.

"It is nice," he said quietly. "Kind of hopeful…" he trailed off and gave Dean a long look. He cleared his throat and Dean grimaced at the sound; he knew that sound all too well. He'd been expecting to hear it for the last two months.

"Dean – it's been two months…"

"And?"

"Dean, come on, you've been avoiding me since we got back to Rufus's bunker. Could you just let me talk to you? Please?"

Dean sighed, turning away from his brother. "Look, Sam, I know what you're gonna say. I'm not sleeping, this is eating me up inside, I shouldn't have brought you back, I was stupid to sell me soul, blah, blah, blah. Just – spare me the chick flick, alright? I'm fine. You're alive. We've got monsters to kill and a psycho to overthrow. Let's focus on that."

Sam didn't respond and Dean frowned. Sam was not the type to just drop something so easily. He turned around – not sure if he was going to tell Sam to let it go or maybe just try to start a fight so Sam would forget it – and blinked.

Sam was gone.

"Sam?" he took a step forward, "Sammy? Sam!?"

When he screamed Sam's name the others realized something was wrong and surrounded him.

"What happened?" Grace asked. "Where'd he go?"

"What's that smell?" Tony wrinkled his nose as he stood next to Dean. "It's like… rotten eggs…"

"Sulfur…" Dean whispered. "Oh no, no, no, no… SAM!?"

~/.\~

Sam's head was pounding furiously when he woke up. He started trying to get his bearings as soon as he became conscious. He lifted his head slowly and blinked the spots away from his vision. He was in some room – it had metal walls and blood stains on the floor. That was never good.

He was restrained in what he thought was a dentist's chair and there was a tray of shining silver tools next to him. He swallowed heavily and tugged at the leather straps on his wrists.

"Hello?" he called out, clearing his throat. "Hey? Anyone there?"

Something tipped over and he heard the faint sound of footsteps behind him before a soft voice spoke and hands clapped down on the top of the chair, above his head.

"Sam Winchester," the man said. "I've heard a lot about you. We've got so much to talk about…"

Sam blinked and craned his head, trying to see the man behind him. "Who are you?"

"My name is Alistair," he said, "You wouldn't have heard of me… Now, you don't want to be here. I don't want to be here. If you cooperate this will go smoothly and you'll be out of here in no time."

"Cooperate?"

Sam could almost hear the shark-like smile in the man's voice. "Let's discuss the finer details…"

~/.\~

It was cold where Jake woke up and it took him several seconds to open his eyes. The room was mostly dark, metal on metal. He tried to sit up and realized that he was strapped down to a chair. Twisting his head around, he realized it looked vaguely like a dentist's chair and the tray of sharp tools next to him made his stomach lurch.

When he heard footsteps echoing on the metallic floors he expected to see the yellow eyed man from his nightmares. He wasn't expecting the normal looking man in a suit to approach him with a steely smile on his face.

"Who are you?"

"Jake Talley," the man said, "I've heard some interesting stories about you. You're the dark horse in this race, Jake. If you wanna win, you're gonna have to step it up…"

~/.\~

Michelle shivered as she walked down the corridor to the prisoners' cells. The Master had lowered the temperature to near freezing in the last day and seemed intent on leaving it there. In spite of Lucy Saxon's conviction, the Master had not calmed down since hearing of his wife's pregnancy. Michelle wouldn't say that he was angrier after hearing the news, but he certainly wasn't happier.

"Michelle!" Jenny Sheppard was the only one awake when she came down, but Lassiter, Sally and Lestrade were roused soon by her exclamation. She hoisted a set of blankets in her arms and smiled at them.

"I thought you might want these," she said, "Stole them from the guards' quarters."

"Won't you get in trouble for that?" Jenny asked, accepting the blankets she passed through to her and Lassiter. Michelle shrugged and turned to give blankets to Lestrade and Sally. She didn't say anything when she met Lestrade's eyes, but she knew they were both thinking the same thing: it was a miracle he and Sally were still alive and with current events the way they were, it wasn't going to be for much longer.

"I doubt he'll notice," she said, "not with the mood he's been in lately. They're really working down bellow. We've been finding dead Toclafane for the past couple of weeks, just scattered in places."

"How many?" Lassiter asked, eyes bright as he wrapped a grey blanket around himself to help the shivering.

"Not many," Michelle admitted, "A few dozen. It's enough to get the Master's attention though. He's furious." Her eyes lifted upward for a second, "He's filming another one of his broadcasts… The Doctor won't even scream."

Sally drew her blanket closer, frowning, "That explains the new ice age then. At least they're fighting back."

"How's Lucy doing?" Lestrade asked. News of her pregnancy had traveled around the ship fairly quickly once the Master found out. Mostly, everyone was worried about the woman – she wasn't exactly the picture of mental health and the child she was carrying wasn't human. Not to mention how thin she was and the fact that the bruises on her arms and face rarely had a chance to fade before new ones showed up.

"She's still floating around like nothing's wrong," she said. "She seems to think this baby is going to make everything just go away."

"She's crazy," Sally said, "Absolutely crazy. He'd just as quickly kill the poor thing as he would welcome it like some sick prodigy."

Michelle nodded. Somewhere above a whistle sounded and she sighed, "I'll come back later tonight, when I get the chance. I've got to go."

~/.\~

The Doctor leaned against the wall, breathing heavily. Blood stained the blue shirt he was wearing and it was torn at the collar. The Master cut the cameras and practically threw everyone else out of the room, muttering under his breath.

Pushing himself up, the Doctor shook his head at the Master.

"They're just getting started," he said. His words slurred a bit from the pain he was in. "They aren't going to stop. I told you, they'll keep fighting back. They'll find new ways to kill the Toclafane. New ways to stand up to you."

The Master's lips curled in annoyance, but before he could say anything, Lucy came into the room. For the first time in two months her expression wasn't one of strangely distant joy. Her face was screwed up in pain and she had her arm wrapped around her stomach tightly.

"Harry…" she croaked out, her voice cracking. "Harry something's wrong…"

The Doctor stared as she stumbled in, barefoot again. He sucked in a sharp breath as she looked to her husband with wide eyes. There were bright red spots on the ground at her feet, trailing down her legs and forming a small pool.

"Something's wrong," she repeated. "Harry, something's wrong with the baby!"

~/.\~

A/N: I feel awful for writing that. It was actually really difficult to write, but definitely effective. And thanks goes to KMW1968 for giving me the idea of Lucy miscarrying; it certainly does help explain Lucy's character and the trauma she went through.

I did a lot of research of miscarriages for this; even though I didn't go into detail, I wanted to have everything right and know exactly what I was writing.

This felt like a slow chapter… I'm not sure why, but still.

Thanks for reading! And Happy New Year guys!

Please don't forget to review!