Thank you so much for the reviews/favourites for the prologue! I'm happy to see there are people out there wanting to read this. :) Sorry for the wait, parts 2 and 3 grew way beyond my expectation, but I hate rushing beginnings because I believe it's crucially important to set a story up properly. Anyway, part 2 might not be up until Friday due to its ridiculous length (20 pages... no, I don't know how that happened either) and my work schedule.

For any of you, who might read the prologue before I edited the author's notes, this story will also cross over with "Agents of SHEILD", but there won't be any spoilers for anything past the first episode of season 2. I won't be dealing with their main plot at all, mostly with characters and the aftermath of season 1.

THREADS

No one took any notice of her as she walked through the halls: long blonde hair tied into a perfect tight bun that fit just beneath her hat, minimal make-up (enough to accentuate, not enough to be noticeable), air force uniform with a gold leaf on her shoulder completed with a regulation-length pencil skirt, sheer nylons and sensible one and a half inch heels. She walked with her head held high, confidently and with the regular gait of a soldier, but quiet – a seasoned soldier would probably take one look and guess special ops. They wouldn't be too far off the mark either.

That was image the Black Widow carefully presented to those she passed by in the halls of the Pentagon. However, it was what they didn't see that was important.

In her left hand she held a briefcase full of reports that, while real enough and probably important to someone, were of no actual significance to her mission and there was certainly no one waiting for them inside this building. The sleeves of her uniform jacket were just long enough to cover the widow's bites she wore underneath. The last button could be also be easily torn off and act as a short-distance surveillance device. Her eyeglasses contained a hidden camera and communicator – it didn't have much of a range, but it didn't need to.

Her mark was a General Markham. Or rather, his office was. Hydra hadn't lost all their military backing, they had evidence of that, but they needed to figure out who those backers were. Their only potential ally, General Talbot, was treating all former SHIELD agents as the enemy, including her, despite having been one of the people to expose the threat in the first place.

Oh well, her methods were more interesting anyway.

Then she heard voices coming from a door on her right. Loud voices. An argument? They were muffled behind a door, but the emotions were obvious. The word 'Hydra' had Natasha tripping over nothing in particular – oops clumsy moment – and then pausing as she checked the heel of her shoe, nudging it as though to make sure it hadn't come loose. Just in case someone was watching the cameras. Meanwhile, she ran her other hand over the last button, pressing it lightly to turn on the recording.

"-until this Hydra mess is sorted out!"

"Jack, I know Hydra's a problem! But you and I both know that it's not the biggest problem we have right now. The SGC has obligations to our allies and this is breaking those obligations!"

"It doesn't matter! Orders are orders, Daniel, you've been working for the Air Force long enough to know that! Everything stays grounded until Hydra is rooted out completely."

"Hydra won't matter if the Ori get this far!"

There were a few moments of silence. Natasha let go of her shoe. She straightened her blazer, running her hands over the front of it, tearing off the last button with the flick of a finger and letting it fall to the ground. She adjusted her glasses as she continued down the hallway, activating the nearly-invisible listening device in her ear.

"-still have time-"

"No Jack, we don't! According to the our latest intell, they're planning a large-scale assault and they're planning it soon. And right now, we're in no shape to fight back. Sam's working on her idea, but she's not sure she can make it viable quickly enough. The chair-"

"Enough! Daniel, I know exactly where we stand with this. I've seen every single, dismal report-"

"Yes, but have you actually read them?"

"Yes, as a matter of fact I have. For once. And a dyson vacuum doesn't suck this much, but I'm under orders just as much as you are. Do you think I haven't fought it?"

A sigh. "I know, Jack, but... Is there anything I can do? I know I'm not exactly the Joint Chiefs' greatest friend right now after that whole Hulk thing, but what if I talked to them? I could go in front of the IOA, the Pentagon, anyone. I'll do anything. We need to do something. It's not just... morale is horrible at the SGC. It was bad after New York, but now? Now it's worse."

"Look, I'll talk to Hammond and see what he says."

"Okay. I'm actually meeting him for dinner tomorrow so I'll bring it up then."

"Still going to New York next week?"

A deep breath. "Yeah. I-I have to. Cassie's going to fly up to spend the weekend with me. We'll go to the museum together on Friday."

"Good. That's... good. Wish I could go too, but well the president wants me here in case they uncover Hydra ties somewhere. Or something. Don't worry, the SGC has good people; they'll pull through."

"No, they have pulled through. They've done amazing things. They should've been allowed to continue to do amazing things – the things they trained for – instead of getting sidelined in the name of maintaining secrecy. And right now, they're angry, betrayed, frustrated. If the SGC were a ship, I'd call it the Bounty."

"Great. Well, at least I'll know who to blame if that mutiny ever happens. Hope you at least get yourself an eyepatch and a parrot. Or would that be a camel, since it's you?"

"You're hilarious, Jack."

The conversation continued as Natasha slipped into General Markham's office, but not for long. The two men left for lunch together just as she was logging into Markham's computer. On her way out, she picked up the dropped button. No one paid her anymore attention as she was leaving than they had when she'd arrived. Mission accomplished.

She walked down the steps from the Pentagon and hailed a cab, asking it to take her to a little Italian restaurant she knew of. It wasn't far and less than ten minutes later, she was paying the cabbie and getting out at her destination. Once out of the cab, she made a show of checking her watch, looking around and then checking her cellphone messages until the cab had driven away. Only then did she walk under the restaurant's canopy and used its shadow to slip into the alley beside it.

The backpack she'd hidden there last night was still stuffed behind a stack of plywood. It took her a matter of minutes to pull her hair out of its bun and clip on a bright pink hair streak, slip in a fake nose ring and change her blazer, pencil skirt and sensible heels for a Washington U sweatshirt, grungy, torn jeans and converse sneakers. She stuffed the uniform into the backpack, along with the glasses and hefted it over her shoulder. Then she walked out the other side of the alley, slouching slightly as she walked to the busstop on the corner.

Two minutes later, she boarded a city bus.

An hour and forty-three minutes after she'd walked into the Pentagon, the Black Widow was sitting in front of a Starbucks with a veritable tub of coffee in front of her as she used her tablet to tap into their wifi.

A few minutes later a purple nike gym bag was thrown onto the ground next to her backpack. "Hey long time no see," said a familiar voice.

Natasha looked up and smiled in surprise at the blond man standing in front of her table. "Oh my god, it's good to see you!" she exclaimed with a bubbly smile and stood to hug the newcomer. "How's it going?"

"Not bad, nothing to write home about, but you know," he replied smoothly, his shrug a bit stiff (probably due to the kevlar vest underneath the black t-shirt and leather jacket). His jeans weren't quite as grungy as hers, but they had a well-worn look to them.

In other words, she hadn't been followed.

She gestured to the other chair. "Have a seat."

"Hang on, let me get a coffee first."

While Natasha waited for Clint to get himself coffee and a sandwich (he'd been staking out the Pentagon since early this morning in case she needed back up so was probably quite hungry), she casually scanned the street for anything suspicious.

"So, how did things go on your end?" Clint asked after he'd sat down with coffee and a ham and swiss sandwich.

Natasha shrugged. "I have the information, but from what I've seen so far, I think Markham's a bust. No idea how he managed to make general, but it wasn't Hydra."

"Damn, well one name crossed off the list, I guess."

"Hm. I did, however, come across something else that was interesting."

"Oh?"

Natasha dug into the front pocket of her backpack and pulled out an mp3 player. She pretended to fiddle with it for a few moments, while she slipped the button recorder into a slot at the bottom. She handed it over to Clint, who took it and immediately put the headphones on and began. She watched his reactions while she watched their surroundings out of the corner of her eye.

When the conversation finished, Clint stopped the playback and took off the headphones. He looked thoughtful while Natasha put them back into her bag.

"You're definitely right," he finally said when she was done. "That was interesting. I gotta say, something that's potentially a bigger threat than Hydra doesn't sound good. Also, can't say I've ever heard of the military using the acronym SGC... could stand for anything."

She nodded. "Same as IOA."

"International something something, or maybe Internal... 'A' cold stand for 'association' or 'administration' maybe?"

"Maybe."

"Do you know who either of them are?"

"The plaque on the office door said Leutenent General Jack O'Neill."

"And this Daniel guy?"

"We have just under a week to figure it out."

Clint's eyebrows rose. "Does this mean we're going to New York?"

"Unless you have something better to do?"

"Nope."

"Mac says everything's working fine as far as he can see, and Trip has swept it for every type of surveillance devices they could think of and then some," May continued.

Coulson nodded thoughtfully. "And Skye tells me it's clear of any sort of radio signals."

"Which means...?" May raised an eyebrow at him.

The corners of Coulson's mouth twitched slightly. "Which means we have ourselves a quinjet."

"But at what cost?"

Coulson took a deep breath, his face sliding back into its habitual neutral expression. "At a cost the agents involved were willing to pay. That all of us are willing to pay."

"Was it worth it?"

"Yes. Or rather, we'll have to make it worth it. That's our job now; to make sure that every person who sacrifices their lives... any part of themselves for SHIELD doesn't die in vain."

May nodded, her posture relaxing slightly even as her expression stayed just as severe. "I had to ask."

Coulson nodded. "I know. You wouldn't be much of a second if you didn't." He took a deep breath and adjusted his tie. "Well, shall we go take a look at what Skye has for us?"

May inclined her head and stepped aside. "After you," she said with a slight smirk.

Downstairs in the main room, they found Skye sitting crosslegged on top of the large conference table, furiously typing. She looked up when she heard them coming down the stairs and smiled. The others were sprawled around the room in various states of relaxation, Lance and Mac with their usual beers in hand. Coulson nearly rolled his eyes at their poorly-hidden attempts to appear uninterested in Skye's report.

"Heya boss man, that didn't take you nearly as long as I thought it would," Skye called to him.

"Does that mean you're not ready to present your findings?" he asked.

"Wouldn't have called you if I wasn't."

"Good, then what do you have?"

Skye bit her lip and hesitated for a moment. "Okay, so before I start I should probably mention that I'm not actually sure what I've found. Suspicious, super-secretive: yes, definitely. Evil and affiliated with Hydra: maybe, maybe not."

"Why don't you start from the beginning, Skye," May prompted her.

"And the rest of you might as well stop pretending you're not listening to every word and pull up closer," said Coulson.

Skye waited for the others to come in closer before bringing her research up onto the projector.

"Okay, so as you all know I've been scouring any and all military communications, databases, reports, ecetera for any evidence of Hydra activity. Well, I came across a couple of references for something called Project Blue Book, which you know, sounds totally innocuous."

"Which means it's probably anything but," Lance added.

Skye's lips quirked. "Exactly. Anyway, I did some digging and saw it referred to in a few other places – sometimes also called the SGC. And this is where this whole thing gets really weird and confusing." She brought up a few other files, opened the reports for them to see. "Because the more I read about this project, the less I understand. It's almost like it's written in code and you need a cipher or maybe a legend to understand it. Like here-" She highlighted a section of the text. "-it's referring to something called 'naquadah'. I have no idea what that is. A few of the reports mention mines so I guess that means it's a mineral or a metal or rock or something-"

"Could be a code word for 'diamond' or 'gold'," May suggested.

Skye nodded. "That's sort of what I'm thinking. And that's one example. A lot of the reports are like that. Or here they're talking about the 'people from the Land of Light', also refered to as P3X-797."

"I see what you mean," said Coulson, his eyes skimming what he could see of the reports on the projection screen. "It's like they're written specifically for people who know what's going on. Or who possess the cipher to decode it with. There were a few operations SHIELD handled that way."

"Really?" Trip asked.

Coulson smiled thinly. "There weren't many, but some yes. It's useful for misdirecting people who go snooping where they shouldn't."

"Yeah, well, as the person doing the snooping here, it's damn frustrating," said Skye. "Anyway, I decided to try it from a different angle and from what I've managed to figure out, whatever this Project Blue Book is, it's got ties to Cheyenne Mountain in Colorado Springs."

May raised an eyebrow in surprise. "The air force base?"

"NORAD?" Trip said at almost the same time. "This is affiliated with NORAD?!"

Skye paused. "Uh, same complex as NORAD, but I didn't find any evidence to suggest they were in any way connected other than sharing space."

"I think there was supposed to be an old missile silo underneath NORAD," said Coulson thoughtfully. "They could be using that space for the project."

"That... would make a lot of sense actually," said Skye. "'Cause this Project Blue Book/SGC thing? It gets weirder."

"Great," said Lance. "I just love it when the weird things get weirder."

Skye brought up a few more reports. "I hacked my way in through government channels and found a few funding reports." She brought them up. "Whatever's going on down there has been eating money; like huge chunks of the military and Department of Defense's budget has been going towards this thing."

Trip whistled in awe. "Jesus, girl, this thing's gotta be big for the government to pour that much money into it. What is this, research? Weapon's development?"

"I have no idea, but the number of civilians associated with it is ridiculous – and super random. I found a list of people from medical experts and biologists to physicists, engineers and even a whole bunch of archaeologists and linguists. Also, oddly enough, a handful of diplomats."

Coulson blinked. "That is an odd mixture. Any clues at all what they're doing down there?"

Skye shook her head. "They're building or developing something that's for sure. Something that's taking a lot of power. Here, check out the power drain from this place."

"Well, it definitely looks like something that deserves a closer look," said May carefully. "Skye, do you have a possible in for us?"

Skye grinned. "Now that is a question I can answer." She closed the document windows on the projector and replaced them with a personalle file, complete with ID photo. "Meet Doctor Daniel Jackson, double PhD in archaeology and linguistics and civilian consultant with the SGC. Was hired on to the project eleven years ago and has been with it ever since with three note-worthy gaps in his record."

"Gaps?" Colson asked. "What sort of gaps?"

Skye's grin widened. "He was dead."

"He was dead," Colson dead-panned back at her.

"Say what?" said Trip. "Seriously?"

"Seriously," said Skye. "According to his record, Doctor Jackson has been declared dead not once, not twice, but three times."

"Guess you're not so special anymore, Director Coulson," Lance drawled.

"I suppose not," said Coulson with a thoughtful frown. "I know everyone jokes about so-called 'military intelligence', but that's a bit much."

"That's what I thought," Skye agreed. She winced slightly. "Unfortunately his file is heavily redacted and really well protected. I had to pull back when I realized I was about to get caught in a tracer program, so I don't really have any details... But, I thought I recognized the name, so I did a basic google search."

Skye's fingers flew over the keyboard and a few seconds later the projection screen showed a webpage. It was simple, obviously put together by an amateur. May's eyebrows raised at it in surprise. Coulson blinked.

"He's a conspiracy theorist?" he asked.

Skye shook her head. "Not him personally, but his work is used by conspiracy theorists. As far as I can tell he doesn't personally have anything to do with any of the sites I found and only a few had any relevant information about him – I think, like, maybe one or two had made the top-secret government job connection. In his Phd thesis he theorized that Egyptian culture was actually a lot older than we think. Also, he talked about, uh-" She consulted her notes. "-cross-culture pollination and how disparate cultures that never would've had any contact nonetheless developed similarities. He doesn't actually mention aliens himself, but the consensus is that it would've been the next step in his thought process. He got laughed out of the archaeological community for it and hasn't published anything since."

"That we know of," Coulson added.

Skye paused. "Right, sure, that we know of."

"Disenfranchised, with crazy theories and a knowledge of languages and ancient myths..." Trip began. "He sure sounds like the kinda guy Hydra would be looking to recruit."

Coulson looked to Skye. Skye nodded to the room at large. "Yeah, on paper he looks like the perfect candidate for Hydra... except for one huge blip. Remember that thing with the Hulk a few months ago? The one where Ross got demoted and the Hulkbusters disbanded because he fired on a civilian target and didn't give a shit?"

Everyone nodded.

"That was Jackson?" May asked.

"Yup, that was Jackson. I mean, could be he was just pissed that his friend's adopted daughter nearly got killed, but tactically it would've been a really bad move on Hydra's part."

"Agreed," said Coulson. "Hulk on the run keeps at least one of the Avengers out of the picture. According to a source of mine, Bruce Banner is now back living in Stark Tower."

"So, other than making our heads explode, is there a reason we're learning about this Jackson guy?" Lance asked.

"I'm not sure that breaking into Cheyenne Mountain is really all that feasible at the moment," said Coulson.

Skye smiled brightly. "Well then it's a good thing he's not in Colorado Springs right now. According to his credit card statement, he's in Washington this week."

"It'll be risky," said Coulson thoughtfully. "He had some pretty heavy-hitting political allies in his case against Ross. I'm not sure I want to stir that hornet's nest just yet."

"You've got something more, don't you?" May asked Skye.

Skye smirked. "Yup," she answered, popping the 'p'. "From Washington he's got a commercial flight booked for New York on Thursday. Our best guess for grabbing him is Friday."

"Why Friday?" asked Coulson.

"It's the anniversary of his parents' death. He's going to be in either one of two places: the cemetery where they're buried, or the museum where they died."

Sam paused in front of the guest room and went over what he wanted to say once more in his head. He felt slightly ridiculous bracing himself as if for battle when the closest thing to a weapon he had were the hot rum toddies his mom had made, and the person he was about to face was a close friend. But only slightly ridiculous, because said friend was Steve Rogers, Captain America himself. And Steve Rogers was one stubborn son-of-a-bitch.

"Hey," he said when he walked into the room.

Steve turned away from the window (not exactly a hardship, since the neighbour's yard didn't exactly make for picturesque viewing unless you were into scrap-pile chic) and smiled at the mugs Sam was holding. He shook his head.

"Your mother is an amazing woman," he said.

"Yeah, well, in case you haven't noticed she's pretty much adopted you," Sam drawled as he handed him one of the mugs, snickering at the way Steve's ears turned pink in embarrassment.

Steve tried to hide a pleased little smile by taking a drink of his hot toddy, but Sam saw it anyway. He grinned. Then cleared his throat.

"Speaking of my mom, she's worried about you." It was cowardly, but Sam wasn't above using slightly under-handed methods if it meant ensuring the well-being of his friends. Besides, it wasn't completely false.

Steve frowned. "What do you mean?"

"I mean you've been pushing yourself too hard. You need to take a break, man."

And, yup, there it was: that flash of stubborn pride. "I'm fine," came the clipped reply.

"Yeah, you're really not. Look, I get that you really want to find Bucky, I do. But we've looked through every damn city, town and hamlet between Washington and New York and spent the last two weeks scouring Brooklyn in case he wanted to find something he recognized. And we've got nothing. We don't even know that we're on the right side of the Canadian boarder or that the Winter Soldier got enough of his memories back to remember Brooklyn as home. Hell, for all we know, he had an extraction plan that somehow didn't fall through and he's now back in Russia or something!"

Steve's eyes flashed with pain, his lips turning downwards unhappily. "Sam, if this is-"

Sam raised a palm out to stop him. "I'm not saying we should stop. I told you I'd go wherever you did and I meant it. I'm not abandoning your mission anymore than you are. Just... I'm just suggesting a break."

Steve opened his mouth to protest.

"One day," Sam cut him off again. "That's all I'm saying. Let's take one day to relax, clear our heads, recharge and then plan our attack from there."

Steve didn't look thrilled about the idea, but at least he'd stopped protesting. For the moment. Deciding to press his advantage while he could, Sam pulled the leaflet he'd found sitting on top of the newspaper pile in the livingroom out of his back pocket and showed it to Steve.

"Look, the Met's got a special exhibition on right now featuring art of the Ancient World or something. Apparently they're celebrating the fifty year anniversary of the crown jewel of their Egyptian collection. You like art, right?"

Steve reluctantly took the pamphlet from Sam. "I was an art student before the war," he agreed as he looked it over.

Sam fought to keep the triumphant grin off his face. "So what do you say? Tomorrow's Friday. We take the day off, meander around the Met, maybe catch a movie or go to the zoo or whatever we feel like afterwards and then we can spend the weekend figuring out a plan. Or however long it takes us."

He watched Steve hesitate, obviously tempted, but possibly feeling guilty about it.

"Sometimes stepping away from a problem for a short time and coming back to it with fresh eyes makes it easier to see the solution," he said. "Besides, my mom won't worry as much if she thinks you're taking care of yourself and taking a break when you need it."

Steve rolled his eyes and shot Sam an unamused look. "Sam, you and I both know you're just shamelessly using your mom to get me to say 'yes' to this."

Sam shrugged. "Is it working?"

Steve watched him for a few moments and then finally huffed in a mixture of amusement and frustration. "Yes, alright, fine, let's go to the museum tomorrow."

Sam grinned. "Good, then I haven't used my mom's name in vain after all."

Steve smiled and Sam couldn't help but notice how much more relaxed he looked already as he took another sip of his hot toddy.

Daniel stood on the sidewalk of Fifth Avenue and stared at the long stairway that led to the imposing stone building of the Metropolitan Museum of Art. It wasn't like he hadn't visited the museum since his parents' death, but he'd always managed to avoid most of the Egyptian wing (it often involved 'getting lost' or quietly wandering away from the school group he was with). Just knowing that was his main destination today made his palms sweat and the building before him tower in a way that had his mind flashing back to memories of Ra's hat'ak.

He snorted softly to himself. He was being ridiculous, he knew he was.

He squeezed the cellphone in his pocket. It had Cassie's message on it, the one telling him that she was running about half an hour late, and his reply, saying he'd wait for her inside.

Well, he'd have to walk up those stairs first.

He took a deep breath and let it out slowly. Then he squared his shoulders, pictured himself wearing his kevlar vest and combat boots, and marched up the stairs. The stairs were longer than the ramp at the SGC, but it wasn't like the doors at the end literally led to another world. It was just a building, after all.

And the ghosts that haunted it only existed in his own mind.

See you all on Friday! :)