AN: I've cut the prologue and the first chapter together, making a pretty sizable bit for people who are just starting to read this fanfic. It also makes it so according to fanfiction, chapter 2 isn't chapter 3 for example.
To those just starting this fanfic, have fun! It gets better!
Chapter 1: Past and Present
[Day -192]
"So you're telling me the weirdest thing you've ever seen Coulson do was not his 'alien writing on the wall' phase?" Skye's look of cheerful disbelief as she gripped her glass bottle nearly made May smile herself. Skye was one of the few things besides Coulson that made her smile occasionally, reminded her that she didn't usually.
May continued, glad that Coulson was elsewhere, "We were in Chicago, he started talking to a streetside security camera just like one of those crazy homeless people would"
"What? Was he telling it to take him to it's leader?" Hunter couldn't help but joke, causing Skye to break into a suppressed laugh at the suggestion.
"He wasn't pulling any verbal punches, that's for sure. He was pretty annoyed, by the looks of him" May took another swig of her beer. These evenings were nice, the evenings every few weeks when the good guys finally got a break. It was times like these when she was forced by her teammates to relax, which admittedly was nice. It wasn't as if she could force herself.
"So why was he annoyed at a security camera?" Skye chuckled softly. She loved stories May told about Coulson. She knew Simmons did, too. It was always funny when May portrayed Coulson like he would probably act and then Coulson would 'accidentally' barge in halfway and correct all the details of May's story. Coulson may not have appeared just yet, but she wanted to hear more of the story before he corrected her.
"Well, we were trying to figure out who this Hydra head was in this corporate conference in Chicago a couple months ago, we had no luck so far, and one hour left to find him. That's when Coulson got mad at the camera, as if he was talking to the person behind it, someone watching him specifically. I'll tell you, I thought I was going to have to drag him to the nuthouse. Then, a payphone rang nearby, Coulson ran to answer it, and then excused himself for almost the entire hour and then dragged the guy into an alley at the last minute. I don't know where he went-"
"I was at the library" Coulson interrupted, standing in the doorway to shock everyone with his entrance.
The standard reactions ensued. The "Director"s, the "sir"s, the glancing downward to avoid the awkwardness of having the person you're currently talking about interrupt. Even Skye fell victim to the group mentality, her ears eagerly waiting for Coulson's obligatory correction.
"For the record, the security camera looked funny, and I was making fun of it" Coulson began, Skye having to bite her tongue to prevent herself from bursting out in excessive laughter in the middle of his revised story. "After that, one of my sources sent me coded information based on books encoded with the dewey decimal system at the local library, thus rendering me the identity of the guy we were looking for" Coulson said procedurally, taking a few steps onward to his office.
"and of course he took so long because he was reading the books for character descriptions" May retorted, obviously not believing Coulson's story for a moment. The simplest of smiles on her face betrayed that information to him, a smile shared by close friends when one knew the other was full of shit. Coulson wouldn't tell May the reasoning behind it, and both of them knew that.
"I personally enjoyed 'Of Mice And Men'" Coulson turned, obviously finished with the conversation as his last remark sent the group into raucous laughter. Skye and Simmons weren't the only ones who enjoyed when Coulson attempted to revise the story May was telling about him. The door to Coulson's office opened as the director entered, brushing off the story like it was nothing. Just like keeping the American people from the truth, the key was to let them believe what they wanted to believe. If one denied the truth, then it was quite obviously the truth, and nothing anyone would say could change that.
Unfortunately, as he flicked on the light switch, remembering distinctly how he kept the lights on when he left, Coulson realized the truth might not be hidden for much longer.
Not much could shock Coulson into a practical momentary heart attack, not even May (He had gotten used to it, after all), but when a known psychopath in service to a technological god appears sitting at your desk, you'd find there's nothing else you could really do.
A quick movement of his foot shut the door rather suddenly, never mind what his team might think of him. His hand was quick to the lock, earning but a smile from the genius hacker, "what's the matter, Phil?" she gave him a pouty expression, weird for anyone who didn't know her and creepy to anyone who did, "still haven't told your team about your source of information?"
Coulson managed to get over the shock from Root's jump scare, "this is mainly curiosity talking, but how did you get in here?" The room was sealed when he wasn't here, Fury's toolbox was in a safe, unbeknownst to everyone else, his office was one of the most secure parts of the base. Added to the fact that Root wouldn't have been allowed in the base in the first place...
Root reached to her chest and held up an ID badge on a lanyard, shaking it slightly to draw Coulson's attention to it, "I used the front door. Why? How do you come to work in the evening?" She smiled proudly, dropping it back down again. Coulson had been about to ask how she got it, but dismissed the question. Either she had hacked the database like she normally would or she had actually gone through the interview process without him noticing, which was equally likely. Coulson didn't blame Billy for giving Root a lanyard, but a pang of annoyance at the man went through him for letting her in the base.
Coulson resigned himself to a different question other than how, "why are you here?"
"Don't you remember the deal?" Root tilted her head, reminding Coulson of the deal he made, a deal he once briefly considered going back on. The social security numbers of all the heads of Hydra he was looking for, in exchange for his fealty to a supposed god. He hadn't even believed the woman until the first pay phone rang, leaving him with the social security number of Ward shortly before the death of Billy's brother Eric. It wasn't the machine's fault, he was simply too late to figure it out, too late to prevent Eric's death. Ever since he had nightmares about what the machine's requirement of fealty might mean, whether he would have to become an evil assassin for the machine, whether SHIELD would have to become another Hydra, or even if he had to hurt innocent people. He'd lie awake at night and try to ignore the urge to do more alien writing and be forced to think about it. No matter where he went he'd glance up at a security camera, any random security camera, and realize that the machine had held up it's end of the bargain, while he hadn't. Eventually he would have to be loyal to a very literal deus ex machina.
"I remember the deal. I remember that I'm going to have to work for your machine" Coulson looked Root in the eye, not backing down. He silently regretted the closed circuit surveillance camera he had installed in his office to make sure he could trust everybody on his team. It only just pointed down at the seat of his desk, rendering him out of view, but Root was in the eye of her god, and the machine could without a doubt hear every word he said. "Sorry if I didn't believe you when the deal was made, I might've dismissed the idea of reading the terms and conditions, but if it's anything evil your machine wants me to do-"
"it's not" Root interrupted, "come now, Phil, if the machine wanted to do anything evil, it wouldn't need you, or me, or any of the assets at it's disposal. Remember the flash crash earlier this year?"
"The stock market" Coulson nodded, his fists clenching slightly, "the machine caused that?"
"The machine fixed it, with some help, and some loss" Root paused, glancing to the side. Her vulnerability was only present for the smallest fraction of a second. She hurt, and she lost someone when they fixed the flash crash. "the flash crash was caused by another machine, known as Samaritan"
Coulson thought for a moment, "I've heard something about Samaritan, a whisper or two in the higher up branches of the government after the fall of SHIELD. Wasn't it the government's contingency when SHIELD fell?"
"more like Hydra's. Arnim Zola's algorithm determining a hit list for the three helicarriers was a precursor to Samaritan. Of course, the original programming was made decades before by a neutral programmer, forgotten, and then harnessed by a company called Decima Technologies, one of the many fronts of Hydra. They got government approval, but thankfully before Samaritan went up, we managed to sabotage one of the drives to account for some...errors in Samaritan's operating system. Your name? Your face? Ignored, like mine" Root smiled knowingly, her feet on Coulson's desk, making him slightly uncomfortable. Nobody put their feet on his desk, except him, of course, but Root was one of the few people that could scare him into silence.
"So that's how SHIELD has stayed hidden from Samaritan." Coulson glanced up at the camera which kept watch over his chair, "I suppose another thank you is in order", he looked back at Root, "so I take it SHIELD is now at your disposal?"
"Now now, Phil, SHIELD is at your disposal, not hers" Root tilted her head again -god that smile was creepy when she did it. A normal person had doubts, questions, not Root. Root's smile was creepy because it displayed absolute certainty in what she was doing. Coulson did not want to end up like that -"however, it doesn't change the fact that you're at her disposal, so if SHIELD is at your disposal, then I guess you're technically right" She shrugged
"Well then, shall we get started?" Coulson sat down in front of his desk, resigning himself to his fate. The machine wasn't evil, according to Root. The machine had also been very helpful. He still didn't see why he shouldn't, apart from the obvious nudging voice in the back of his head that claimed it was all a trick. The social security numbers weren't, as they had predicted the identities of Hydra heads with 100% accuracy. Coulson couldn't assume anything without further evidence, and there was only one way to get further evidence.
"I'd love to, Phil, but this wasn't because the machine wanted something. She just wanted to give you a reminder to make sure you hadn't forgotten about your end of the bargain," Root took her feet off his desk, standing.
Coulson furrowed his brow in disappointment. Once he had come to terms with it, he was rather excited about fulfilling his intended purpose for the machine. It would relieve a lot of stress having finally gotten it done, making it so he wouldn't have to lie awake at night questioning his decision to do so. Anxiety about an event was always most prominent before the event, rather than during it, thus was it here. "What, am I not even guaranteed a sneak peek?"
Root smiled knowingly at Coulson as she walked around his desk, "not right now, we're about to be interrupted"
Coulson opened his mouth, confused, but was cut off as a sharp knock resonated through his office door. A single look at Root's knowing expression told him there would be no way he could sneak up on this woman. As he got up to open the door, the thought of any futile possibility of killing Root to end his obligation came to Coulson's mind. Rationally he knew that the Machine would find some way to exact revenge or, knowing the AI's modus operandi, would simply predict his attempt at murder and relay the information to Root, causing his own demise. Coulson had no intention on acting on this thought, sometimes thoughts came as they pleased, regardless of whether they were wanted.
Skye was waiting outside the door when Coulson unlocked and opened it, "Talbot's on the phone, he says he wants to talk to you." Skye said, noticing Root only seconds later, "oh hey Winifred" she smiled as if she were greeting a friend, "thought you'd have clocked out by now"
"Actually, I was talking to Director Coulson about some possible vacation time" Root talked in a higher pitched, more relaxed voice, smiling a whole lot more broadly than she had in the past several minutes. Coulson had to admire her change of face. She would make an excellent Shield agent with Broadway-level acting skills like that. "Not that I don't love the job and all, but I have some friends I need to take care of and they're kind of lost without me"
Skye nodded, smiling, "I know the feeling, sometimes I wonder how far off the mark these guys would be without me around" They both laughed, making Coulson feel a bit awkward as he cleared his throat, getting their attention.
"I will actually be leaving after I finish some paperwork in the lab, though. Gotta end the night on a high note." Root turned to Coulson, who had momentarily forgot her true identity as a psychopathic killer-for-hire on a mission from god, "You better talk with Talbot, I'm sure it'll be something important" she smiled innocently, not fooling Coulson.
"Have fun with your time off" he said dryly, "Who could possibly predict what might happen?" Coulson joked, making the corner of Root's mouth rise slightly as she turned to the door.
"So how long do you think you'll be gone?" Skye asked Root, following her through the doorway as she closed it, "I'm not saying I'll miss you, but you're the only one on the base who actually gets what I'm talking about most of th-" The door closed, cutting off Skye's last word. Coulson had also forgotten Skye was a pretty decent computer hacker herself, and with Root around, the two must be having conversations the other base personnel wouldn't understand.
Coulson would get to Talbot in a moment, Root's visit having put to rest some anxiety in his mind, but as he looked up into the lens of the security camera over his desk, he took the time to wonder how insane things with Root's machine might become.
There was at least someone- rather, something- in the room who knew the depth to which things could possibly go.
[Day 0]
The past few months had been barely controlled chaos. Skye gained inexplicable powers, another sect of Shield had made themselves known by taking over Coulson's sect for a short time, Stark's robot, Ultron, had tried to destroy the world, thus requiring the initiation of Theta Protocol, Jaiying had tried to destroy Shield with a small army of powered people...quite a productive period of time, Coulson thought. The funny part was that even Hydra was refraining from growing any new heads. Surely, this meant that they were and Shield didn't know it yet, but that would be dealt with. For the moment, however, Shield had some breathing room and peace. For the moment.
Coulson relaxed, finding nothing impending on his schedule. How long ago had he last taken some well-needed vacation time? It was only natural that the next disastrous evil would pop up when he did. No rest for the wicked, after all. He leaned back in his chair, closing his eyes, when a series of short knocks disturbed his short rest. Skye was standing in the doorway, looking at him expectantly.
"Hey, Coulson" she said, a peaceful tone in her voice. That was a good sign. "Mind coming to the loading dock? Some guy wants you to sign for something"
Coulson narrowed his eyes, "I never ordered anything, maybe someone from the other departments?" Fitz or Simmons, maybe, ordering stuff they needed for certain experiments. Why would his signature be required? It never had been.
"Yeah, that's what I thought, but apparently it was ordered for you, so..." Skye leaned against the doorframe, her eyebrows goading him into movement.
"Fine, but I'm a little hands off when it comes to signing forms" He held up his one good hand as he stood, earning a smile and a roll of the eyes from Skye.
"Will you quit with the jokes? They're a bit one-handed" Skye said, then paused, stopping. "I did not mean to say that, I'm serious" Coulson smiled at her reaction. Skye was a good agent, but sometimes she was less tactful than she normally was.
The walk to the loading dock was a relatively quick one, Skye filling Coulson in on daily updates, chatter about coworkers, etc. Coulson noticed the delivery man instantly when they walked outside, a name tag identifying him as "Dennis" on his chest, holding a clipboard, "Phil Coulson?" He asked, checking the clipboard and holding it out to him, "sign here"
"I never order pizza, much less..." He looked down at the clipboard, "various high quality computer supplies?" Coulson narrowed his eyes at Dennis and turned to look at Skye, "Do you know anything about this?" He asked, meriting only a shake of Skye's head, to which he turned back to Dennis, "Am I required to sign it or can you just leave with it? If I'm required, signature might be a little messy" He gestured to his stump of a wrist, still in its sling.
Dennis chuckled, "you should get a hook and an eye patch" he joked
"That's what I've been telling him" Skye spoke up, ignoring the look Coulson was definitely giving her.
"As for if you don't wanna sign, there's another cosigner on the order, Wi-" Dennis began, interrupted by a high-pitched voice from afar.
"That's for me! Sorry!" Coulson turned his head and his heart sank into his chest as Root jogged across the street and up to the building, lunch bag tucked under her arm as she hurried over.
"Winifred!" Skye smiled cheerfully, enveloping the other woman in a friendly hug, "finally back?"
"to stay, thank god" Root gave Coulson a knowing glance as she turned to Dennis, holding her lunch bag behind her for Skye to hold while she grabbed the pen provided with the clipboard, glancing over her shoulder nonchalantly, as if she was being followed.
"I take it you're Winifred Burkle?" Dennis smiled, "maybe next time you should let your boss know when you're ordering something, it'll make for less confusion"
"I know I should, I just like to surprise him sometimes" Root finished her signature, handing Dennis the clipboard, "give my regards to Caleb" She smiled as Dennis tipped his hat to them, opening the back of his truck to have the precious cargo unloaded by the base's staff.
A nagging thought tugged at Coulson's mind, "Exactly how much did all this cost?"
"Not a cent, I know the CEO of the company that manufactures this stuff" Root smiled, "he's more than willing to help me out whenever I need."
Skye nodded, "so, if I were to mention my need for a new laptop...?"
"I wish, Skye, but this kinda stuff is for a special project, and if I were to order stuff for personal reasons, that'd just be dishonest" Root turned to Coulson, "also, some new clients of ours should show up soon, tomorrow at the earliest"
"Wait" Skye interjected, "Shield does clients now?"
Coulson shrugged. Shield wasn't a mercenary group, serving clients to survive. They were a cause, a banner for keeping the world safe. Coulson was just as confused as Skye was, but his deal with the machine made him go with it, "apparently we do"
"They're the ones who are going to be administrating this new project" Root explained, starting to walk off inside the base with Skye and Coulson following, "it's a new kind of advanced supercomputer I've been interested in working on"
"Advanced supercomputer?" Skye raised an eyebrow, "I'd love to check that out"
Root gave a glancing smile at her friend, the thought occurring to her that, aside from Reese, Harold, and detective Fusco, she really didn't have any friends. Sameen was...well, Sameen was Sameen, enough said. Skye was one of the first lasting friends she'd ever had since grade school. They'd only hung out three times, now included, but the two of them were rather close, a type of friendship that just happened without any work having to be put into it. Skye Root didn't want to lose, on account of being the one casual normal (though neither of them were normal) thing in her life.
"Unfortunately, access is going to be restricted" Root didn't turn back, not wanting to see Skye's disappointed face, it could be quite tempting to give in to her at times, and Root didn't exactly want Skye in on her job. "For the most part, access and critical knowledge will be with our clients, Director Coulson, and me, and I'll be the only Shield agent doing the work with our clients. They're perfectly capable of accomplishing their objective on their own, they just need a suitable investor to provide a place to do so"
"So we're investors now?" Coulson asked, stopping outside his office.
"Well, when you put it that way-" Root began, cut off by Coulson.
"when you put it that way, it seems like we'll be getting something out of this" Coulson hadn't meant to phrase it quite that way, but nevertheless, it slipped. He reminded himself that just as Root had to act, so did he. He had to act like she was a normal agent under his command, and he knew if Skye had hired on clients without his permission for a project he knew nothing about, he wouldn't be easily forgiving. "I doubt we're doing this out of the kindness of our hearts"
Root paused, her cheerful demeanor interrupted by a patronizing look. Luckily, she caught herself before Skye could notice, "As I said, Director" she began slowly, "the project is on a pretty need-to-know basis, so I would love to elaborate on it's advantages privately in your office" she said, a side glance given to Skye.
Skye rolled her eyes, "so I take it that means you're not going to tell me anything?" Root shook her head.
"No, sadly. I do enjoy working with you" Skye seemed to smile at that.
"No time like the present, then" Coulson interrupted, gesturing to his office with his good arm.
Root smiled at Skye, "catch you later!" She began to walk past Coulson, but felt Skye's hand on her arm.
"Hey!" Skye suddenly looked very nervous, pulling her hand away from Root's arm. Coulson had long figured out the look of when Skye was holding it down, looking calm and focused on the outside while absolute chaos reigned inside her head, "I was thinking, maybe we could hang out sometime this weekend? Friday, perhaps?"
Root looked a bit taken aback, surprised by Skye's offer, but regained her composure, "sure, I guess." She returned Skye's smile, "I don't...normally get out much, sorry"
"No, it's fine" Skye nodded, "I can understand that" she crossed her arms, "I don't typically get out much either"
Coulson subconsciously decided that was enough, clearing his throat and turning to walk into his office. Root and Skye said their goodbyes, and the moment Root walked in, Coulson closed the door. "Would I be incorrect in assuming that your associates are our new clients?" He asked, knowing there was no need of formalities with the servant of god.
"Secondary assets of the machine" Root explained, her voice easily dropping back into it's normal tone, "primary assets handled the primary function of the machine, that being stopping incidents of national terrorism. Secondary assets do the same, but with the irrelevant numbers. Ordinary murders and all." She filled in for Coulson as she sat in the chair in front of his desk. "The government has control of primary operations, while your new client has control of secondary operations."
Coulson nodded as he sat down in his chair, thinking on this new information, "Seems a bit complicated"
"Normally we just call them relevant and irrelevant"
"To what?"
"National security" Root answered, "those numbers the government handles are relevant, and those handled by our little group are irrelevant"
Coulson thought some more, "you said you were something different" he observed
"The machine had me classified as an analog interface. I speak for it, and run errands for it, like establishing connections in shield" Root put her feet up on the desk, and just like last time, Coulson was hesitant to stop her. Some things never changed.
One small part of Root's explanation bugged Coulson, a small tingle when one noticed a small detail that meant so much, "when you say 'had'..." He began, then stopped, the implication clicking in his head. Coulson had a hunch why Root had checked to make sure no one had followed her, but if it was true...
Root nodded solemnly, "The machine is dead" her pained words sent Coulson's heart into his stomach, thankfully coming back up with her next phrase, "or so Samaritan believes"
Coulson raised an eyebrow, "I'm guessing long story?" He asked, leaning back as Root simply nodded. If there was one thing he could always assume, it was the fact that there's always one hell of a story.
One long story later, Coulson looked into Root's eyes, analyzing her. The absolute look she used to have was gone, replaced with fear, hope, desperation. It occurred to Coulson that Root might've relied on the machine as a religious person would rely on god. How would a religious person react when given definitive proof their god was dead? Root's god was, more or less, dead, and even if Coulson was opposed to allowing Root to use the Playground to revive the machine, he doubted Root would take no for an answer. Not only that, but Samaritan was still active, and having the machine on their side...
"Alright" he shrugged, "I guess you have my approval to do whatever's necessary. As you said, Samaritan is Hydra, and that makes it our enemy, too"
Root smiled, a genuine heartfelt smile, "thank you, Director" she said, her voice barely above a whisper. Coulson recognized the emotion behind those simple words, and knew why. If what Root told him was true, Shield was the only possible safe haven for her to go to. Coulson couldn't help but smile.
Suddenly the door opened, May walking in, "Coulson, w-" she paused, watching Root quickly take her feet off Coulson's desk. Coulson knew the look in her eyes, he knew that she was onto him. "Winifred" she gave a small friendly smile, changing demeanor with ease, "Skye didn't tell me you were back"
"Sorry" Root smiled, "Coulson wanted to catch me up on what's been going on"
"Well, if I could have a word with Coulson" May said, asking a question with her words, but not her tone.
"I have equipment to put together anyways. Just got back today and all" Root stood, "Thanks again, Director" she smiled, walking out as May sharply shut the door behind her. Coulson winced. May didn't look happy.
"Okay, I may have overlooked her sketchy background when she applied, but you never let anyone put their feet on your desk." May's stare was cold, demanding answers. She was right, and had good reason. Coulson never even let May put her feet on his desk.
"Sketchy background?" Coulson deflected
"Didn't you even notice she's using the credentials of a dead woman?" Now that was interesting. All it would take to unveil her cover would be a picture of the dead woman. Sloppy for sure, which didn't sound like Root. It sounded like something the CIA would do.
"So what's this Winifred Burkle actually look like?" Coulson asked, curious.
"Funnily enough, just like her." May explained, "but I'm not explaining anything else"
"What? Why not?" Coulson narrowed his eyes.
"Because you haven't explained anything on your end." Damn, May knew how to get his attention and force him into doing something, "she put her feet on your desk, Coulson, and you let her. Either you're partaking in a forbidden office relationship, which given your resemblance to Colin Mochrie is extremely unlikely-"
"Hey!"
"or," May continued, ignoring Coulson's outburst, "you're afraid of her"
Coulson stopped, clenching a fist to ignore his desire to deny it instantly, "it's complicated"
"Is it?" May asked sarcastically, giving Coulson a look as if asking him to explain everything.
"it's a long story" Coulson leaned back in his chair, "and you're gonna make me tell it, aren't you?"
May simply nodded, stonefaced as ever as Coulson began to explain.