Jill vs the Intersect
by Justin Jossart
A/N: First off, let me say that this is an AU where Jill was recruited by the CIA before Fulcrum tried to recruit her. Obviously, for the sake of the story, she chose the CIA. Originally, this story was going to be a Charah fic, where Sarah trained Chuck to be a field agent. However, I realized that there were really no Chuck/Jill (hereafter known as Chill) stories on the entire site, something I decided to remedy. As it turns out, it was a good idea. Writing Jill's evolving relationships with Chuck, Ellie, and Morgan promises to be very intriguing, and I hope that you find it just as interesting as I do. I also really look forward to watching Chuck "fall down the rabbit hole," and Jill's inner turmoil as she plunges him ever deeper.
Summary: CIA Agent Jill Roberts, asset protection specialist, receives a new assignment: Protect and train the Intersect. With no choice but to accept, Jill struggles not to compromise herself while she trains her ex-boyfriend to be a cold-blooded assassin. A/U Chuck/Jill
Chapter One
"The Director will see you now."
Jill nodded at the pretty blonde secretary and took a deep breath to steady her nerves. In her five years with the CIA, she had only spoken to Director Graham once, and that was only a debriefing. The office was cool, air conditioned to a perfect sixty-five degrees, but her palms were coated in a fine sheen of sweat. She had been unceremoniously recalled from her assignment, ushered aboard an immediate flight from Brazil to DC, and had been driven straight from the airport to Graham's office. She and her partner had been on the verge of unmasking half a dozen Fulcrum agents operating out of a cell in Sao Paulo. Jill knew that the CIA had made Fulcrum one of its top priorities, so whatever was going on had to be big. She brushed a stray strand of long, brown hair behind her ear, acutely aware that she hadn't showered in two days. Her first face to face meeting with her boss, and she looked and smelled like a pig. Great.
With a final, deep breath, she stepped into Graham's office. It was surprisingly well lit, fluorescent overhead lighting banishing any shadows that may have pervaded the room. She didn't know what she had expected... Perhaps a shadowy office that masked the Director's face would have put her more at ease. Instead she was greeted by an office that could have belonged to any manager across the United States. Plaques and certificates lined the walls, while the Stars and Stripes stood proudly in one corner behind the Director's large, but not too large, desk.
The man himself was perusing a file as she entered. Jill was surprised to see that he wasn't alone. Another woman, an older redhead, stood beside the desk, her arms crossed. Jill vaguely recognized her as General Beckman, the woman in charge of the NSA. She motioned for Jill to take a seat in one of the utilitarian chairs directly across from the desk. Still stunned at seeing Beckman in Graham's office, Jill instinctively turned her chair so that she could see both the closed door and the blinded window, all while being able to give the Director and the General her full attention. If Graham noticed, he didn't say anything, instead turning a page in the file he was reading. A stack of similar files sat near at hand. Beckman merely gave Jill a calculating look.
"Agent Roberts," Graham finally greeted. His voice was deep and large, filling up the office. "Thank you for coming in on such short notice." Jill fought the urge to scoff and roll her eyes. As if she'd had a choice. The Director finally closed the file and gave her his undivided attention. "I know that you must wonder why we've pulled you from Brazil." She nodded, but said nothing, so Graham continued. "Tell me, Agent Roberts, what is your relationship with Agent Bryce Larkin?"
Dumbfounded, Jill searched for an answer. "Um... We were at Stanford together, acquainted through a mutual friend. We were both recruited at the same time. After the Farm, he and I went our separate ways, reunited only through a brief partnership two years ago," she recited dutifully.
"Ah, yes. The Madrid mission," Graham mused, stroking his chin. "That was a resounding success, resulting in the destruction of a Fulcrum base and the apprehension or death of more than twenty rogue agents."
"Twenty-two, sir."
"If I recall correctly, Larkin expressed an interest in continuing the partnership, but you declined. Why?"
Jill had no idea what was going on. She'd been flown halfway around the world to talk about Bryce? "After the mission, under the influence of alcohol, Larkin and I... things grew... heated between us." Beckman scowled briefly, but Jill ignored her, forging on. "However, before we could," Jill paused, trying to fight down her blush, "consummate the relationship, Larkin expressed the need to admit something to me, something that I was unable to forgive him for."
Beckman leaned forward, her eyes gleaming. "What did he admit? Had he turned?"
Jill shook her head. "No, nothing like that. Back at Stanford, while he and I were being recruited, Larkin learned that his best friend, my then-boyfriend, was also a CIA candidate. Larkin, convinced that putting Chuck in the field would be a death sentence, fabricated evidence that lead to Chuck's expulsion." Beckman and Graham shared a surprised look, before the Director nodded, urging her to continue. "Chuck and I had dated for two years. Leaving him to join the CIA was one of the hardest things I've had to do, besides turning in my uncle. Chuck's a good person. He had worked hard for his scholarship to Stanford and had a bright future. Larkin took all that away from him."
"Did you have a role in Bartowski's expulsion?"
Jill was shocked. How did Graham know Chuck's last name? What was really going on here? "No. I had no idea he was being recruited until Larkin told me in Spain. I had been under the impression that Chuck had actually cheated and that his expulsion was warranted. Chuck had tried to tell me differently, but I... didn't believe him."
Graham nodded. "How did things end with Bartowski?"
Jill swallowed. She remembered sitting in her dorm, telling her roommate to get rid of Chuck. She had been such a coward, hiding behind Bryce and Rosalie instead of ending things with him face to face. She still remembered the pain and betrayal in his face when Rosalie told him that Jill was dating Bryce. "Sir, I don't mean to be disrespectful, but what does my love life from five years ago have to do with anything?"
"Just answer the question, Agent Roberts."
Glancing at Beckman, who was eyeing her warily, Jill continued. "When I was recruited, I knew that I had to end things with Chuck. I lied to him, fabricating a false relationship between Larkin and myself."
"Why?"
"You don't know Chuck," Jill smiled softly. "If I'd told him I was going away, or had just disappeared, he would have looked for me. He would have spent the last five years turning over every stone until he found me. I wanted him to be able to move on, to find a normal girl, so I made him hate me by telling him I slept with the guy he hated most."
"So Bartowski and Larkin are no longer friends?"
"As far as I know? No. Would you be friends with the guy, your best friend, who got you kicked out of Stanford, crushed your dreams, and stole your girlfriend? It'd be a cold day in Hell before Chuck had anything to do with Bryce."
"Let's change topics," Beckman interrupted. She picked up a file, and Jill could see just enough to realize that it was her own. "You received very high commendations at the Farm, Agent Roberts, particularly in asset protection, asset handling, and undercover work."
"Yes, ma'am. I've never had an asset captured or killed on my watch," Jill affirmed, her chest swelling with pride. "Nor has an enemy agent turned any of my assets."
"How far would you be willing to go to maintain your cover, to control an asset?" Jill hesitated. She knew what the General was asking, but she decided to purposefully misunderstand.
"I passed my Red Test, ma'am. I've had to kill in the line of duty, if that's what your asking. I've burned assets before," she stated. "I don't like it, but I understand that it's part of the job." General Beckman looked conflicted. Technically, the general couldn't order her to have sex with an asset, mark, or agent. It would be a legal shitstorm. However, technicalities were often overlooked in this line of work. Agents often had to say and do things that made their skin crawl. Jill decided to let Beckman off the the hook. "Ma'am, I'm committed to my country. I'll do whatever it takes to complete the mission."
"Good to know," the General replied, her green eyes boring into Jill's brown, before turning to Graham. "I think she'll do."
"Agreed. She's one of my brightest young agents," he replied, giving Jill a rare smile. "Agent Roberts, we have a new mission for you. We're unsure of the mission's length at this time, but you should buckle in for the long haul." Jill swallowed. Long term undercover ops were never pleasant. "Two weeks ago, Agent Larkin stole the Intersect from a high security facility."
Jill gasped. She didn't know what the Intersect was, exactly, only that Fulcrum was desperately searching for it. "Bryce turned?"
"We don't know," Beckman replied coldly. "He may have turned, he may have wanted to sell it, or he may have some ulterior motive we're unaware of at the moment. All we're sure of is that he stole the Intersect and destroyed the original, but was almost immediately apprehended. Before his arrest, Larkin managed to send the Intersect in an encrypted email to one Charles Irving Bartowski."
"The Intersect is more than you know, Agent Roberts. It's a highly sophisticated supercomputer cataloging all of the CIA and NSA's secrets and intelligence. The information is coded into images. There are few people who can see and understand these subliminal messages. It turns out that Bartowski is one of them."
Jill's head was spinning. Chuck was a spy? "General, I don't understand."
"Upon receiving the Intersect, Mr. Bartowski was detained by Agent Walker and Major Casey. He has been in their protective custody ever since. We sent Doctor Zarnow, one of the minds responsible for the Intersect, to try to remove it from Bartowski's head, but we were dealt several... setbacks. Then, late last night, Agent Larkin escaped NSA custody, killing three guards in the process. He's on the run."
"So... you want me to chase down Bryce Larkin?" Jill's heart was pounding in her chest. Capturing Bryce Larkin, one of the CIA's top agents, was far outside of her skill set. She specialized in asset management and protection, while dabbling in sabotage and minor undercover work. She had built her young career on a foundation of turning Fulcrum assets to the CIA, then capturing or killing their handlers.
"No," Graham replied sternly. "You are to head to Burbank, California. You will relieve Agent Walker and Major Casey from the protection detail on Bartowski. They will go after Larkin. You will protect the asset."
"What?" Jill's eyebrows almost disappeared beneath her bangs. "You expect me to protect my ex-boyfriend, who I pretended to cheat on, for an unknown but extended period of time? I won't be able to use a cover! I-"
"Agent Roberts!" Beckman snarled, smacking the desk with a small hand. "Control yourself. We expect you to follow orders."
"I don't understand. Why isn't Chuck sitting in a padded bunker by now?" As much as she hated the idea of Chuck wasting away in a CIA bunker, she couldn't fathom what would keep him out of one. "He's arguably the single most important intelligence asset in the country. Unless..." It suddenly dawned on her. She fought the urge to wretch. "You're using him as bait. You expect Larkin to try to make contact with him."
If the General or Director were bothered by her accusations, they didn't show it. "Yes. However, we want to draw as little... oppositional... attention to Bartowski as possible, which is why we're sending you to Burbank. Officially, you're being honorably discharged from the CIA for medical reasons. To any outside observer, you'll simply be a young woman heading back home and reconnecting with an old flame."
"You'll use your 'severance package' to purchase this home," Graham said, pushing a picture of a typical suburban home across the desk. Jill took it, holding it limply. Everything was moving so fast. "We've used considerable resources to build a sub-basement that will act as a safe room, base of operations and training facility." Jill didn't like where this was going. A special base of operations? How long was this op going to last? "After a brief 'courting period,' Bartowski will move into the base, where you will begin his training."
"Training? What will I be training him in, exactly?"
"Everything," Beckman replied simply. "We no longer have the means to remove the secrets from Bartowski's brain. Our options were to bunker him, kill him, or train him. Agent Walker convinced us of the latter." Jill tried not to show the pain that flared in her chest at the image of Chuck being assassinated, but she didn't think she succeeded. "You will oversee his general training. Periodically, we will send specialized trainers to instruct him in the areas you are unqualified for, as well as test his progress. You'll have eighteen months to transform him from a typical computer geek into a field-ready, fully qualified agent."
"And if I fail?" Jill didn't like the idea of Chuck becoming an agent. He was too good of a person. Bryce was right, being in the field would kill Chuck, but not in the way Larkin thought. It would kill his spirit, not his body. Jill had every confidence that Chuck could become a top agent, but at what cost? CIA agents killed, tortured, seduced and burned assets and other agents alike. She couldn't imagine kind, gentle Charles Bartowski executing someone because they knew too much or torturing information out of a hostile asset.
"Then your 'leave of absence' becomes permanent, and Chuck finds his way to an undisclosed location, never to be seen or heard from again."
Jill stared through the Plexiglas window of a 747 as it touched down in LAX. She'd flown commercial, hoping that the squalling infants and overweight lady in the next seat would keep her from thinking about her assignment, but the distractions did nothing to quell the butterflies in her stomach or the nervous tension in her shoulders. Five years ago, she'd devastated Chuck, choosing the CIA over him. Soon, she'd have to live with him, train him, and protect him. She'd been on some dangerous, difficult missions, but this promised to be her most arduous assignment yet. She didn't know how well she could cope with Chuck's transformation from gentle, loving geek to cold-blooded assassin Worse yet, she'd be responsible for changing him.
"I'm sorry, Chuck," she whispered as the plane glided towards the terminal. At that moment, she truly, deeply, hated Bryce Larkin. It wasn't enough to destroy his life once. No, Bryce had to come around for seconds by sending Chuck the Intersect. Everything that Bryce had done to 'save' Chuck was now pointless; Chuck was going to be a spy anyway. Jill promised herself that she would make sure that Chuck would be the best agent she could possibly make him. He wasn't going to die from lack of training, just a broken heart.
She pulled her carry-on from the luggage rack atop her seat, then deplaned with the rest of the crowd. Most of her fellow passengers made their way towards the luggage carousels, but Jill had traveled light. Her 'severance package' had been substantial; she'd be able to buy an entire wardrobe without making a dent in her new bank account. Even buying the house and a car would be chump change when compared to the overwhelming funds now at her disposal.
Shaking her head, Jill exited the terminal and hailed a cab. She shouldn't be thinking that way. She'd receive no more funds from the CIA for her mission. She'd have to subsist on what they'd already given her for at least the next eighteen months, longer if Walker and Casey failed to bring in Bryce.
"Where to?" The cabby asked, his swarthy face leering at her long, tanned legs. She'd known it had been a bad idea to wear shorts.
"724 Carta Road, Burbank," she replied, ignoring the man's lecherous gaze in the rear-view mirror. Once upon a time, she'd have been bothered. Now, she couldn't care less. She was used to marks and assets staring, touching. This lech wasn't even a blip on her radar. At least she'd be away from all that for the next eighteen months.
Fewer than forty miles separated LAX and Burbank, but with Los Angeles traffic, the trip took over an hour. She was supposed to meet Agent Walker at the home she'd 'purchased,' where they would discuss a place and time for a full briefing with Beckman and Graham. Chuck, as far as Jill knew, was unaware that his protection was being taken over by someone else; she'd see Chuck tomorrow in Major Casey's apartment, which was 'coincidentally' in the same complex that Chuck now resided.
The cabby tried several times to make conversation, starting with a couple of truly horrendous pickup lines. She'd heard both of them in high school from drunken jocks. They hadn't worked when she was intoxicated and sixteen, and they certainly weren't going to work on a CIA agent trained to recognize and resist seduction. She shot the driver a cold glare, one she normally reserved for Fulcrum agents, and he finally received the message. Eventually, she could see the neighborhood where she'd be spending the next year and a half of her life.
When the cab pulled up to 724. she paid the driver, ignoring his clammy hands' attempt to brush against her thigh, and pulled her bag from the trunk. She felt naked without her sidearm, especially walking into a meeting with a fellow, if supposedly friendly, agent. She took a moment to study her new home. It looked much like the rest of the houses around, complete with a white picket fence. It was newer, well cared for, and utterly unremarkable in every way. Perfect. A few brisk strides took her from the sidewalk to the front door. She breathed deeply, schooling her features into an impassive mask, and unlocked the door.
Stepping inside, Jill fumbled for a light switch, illuminating the entryway with a soft golden glow. The house was completely barren, no pictures on the walls or furniture that she could see. The entryway boasted vaulted ceilings and three archways, to the left, right, and straight ahead, while a staircase curved upwards to the second level balcony. Peering through the left arch, she could see what was obviously supposed to be the living room. Grey carpet, unremarkable but soft, covered the floor. Through the right archway was the dining room, which opened up into a rather large kitchen. Marbled counter tops framed the gleaming stainless steel appliances. She noted plenty of cabinet space, and smiled as she ran a hand along the marble island standing proudly in the center of the room. She'd always wanted a kitchen with an island.
The final archway led to a wide hallway, its doors presumably leading to a guest bedroom, the garage, the basement, and a bathroom, while directly across from the arch was a set of sliding glass doors. Jill gasped at the scope of her new back yard. A decent sized swimming pool, surrounded by tasteful stonework, and was that a hot tub? Beyond the stonework lay a well-kept, emerald green lawn, guarded by a high privacy fence. Several large trees shaded much of the yard, their branches swaying slightly in the breeze. She had a hard time keeping herself from feeling giddy. The CIA had given her her dream home. She could imagine kids, her kids, laughing and playing in the yard with the dog before jumping in the pool to escape the hot California summer sun. She'd be lounging by the pool, watching her husband manning the grill. Chuck would turn around and give her that mega-watt smile that curled her-
"Hands where I can see them," a harsh feminine voice ordered, cutting Jill's fantasy short. Jill obediently lifted her hands, palms up, to shoulder height. "Don't move." Small, cold hands efficiently frisked her for weapons, searching everywhere, even places Jill had never thought to stash one. Whoever this woman was, she was a pro. The woman pulled Jill's badge from her back pocket. She could hear the crisp leather open, before the badge was tossed to the stones, landing with a dull smack. "Okay, turn around, but no sudden movements."
Jill turned, keeping her hands in plain view. She tried not to gawk at the stunning beauty in front of her. Long, blonde hair framed a gorgeous face. Perfectly sculpted brows sat atop large, cerulean eyes, a pert nose, and full rosy lips. She suddenly felt frumpy and unattractive in comparison. Jill knew that she was pretty, beautiful even, but this blonde was in another league altogether. It took a moment for the brunette to register the gun pointed at her face. "Code phrase?" The blonde demanded.
"Omega-six-one-alpha," Jill replied, her voice level. "Yours?"
"Two-charlie-seven-November," the woman replied, lowering her gun. Jill couldn't help but notice that the coldness never left the woman's eyes.
"I'd like to see your badge, if it's all the same to you," Jill replied. It never hurt to be careful, especially with such a vital intelligence asset like the Intersect. The blonde still gripped her sidearm tightly, ready for use at any sign of hostility. She all but tossed the badge to Jill, who only needed a few moments to verify the badge as genuine.
"Thank you, Agent Walker," Jill said cordially. Walker still looked like she wanted nothing more than to put a round in her chest. The blonde was silent while she took back her badge, her eyes never leaving Jill's. It was making her nervous.
Finally, after what seemed like an age, Walker relaxed, sliding the gun into the back of her jeans, and extending a hand. Jill, sighing with relief, took it. "Have we met? Your name seems familiar, but I can't quite place it," Walker said.
"Not that I know of," Jill replied shakily, a lump forming in her throat. No doubt Chuck had told her about the infamous, evil Jill who had cheated on him with his best friend before dumping him.
Walker shrugged. "So, what brings you to Burbank?" The blonde asked. "We were only told to meet you here."
Jill nervously swept a loose strand of hair behind her ear. "Sorry, but my orders are to wait for the full debrief tomorrow." It was only half true. Graham and Beckman had given her the option of a full debrief with the entire team, which she had eagerly taken. She didn't want word getting to Chuck that she was coming, preferring to talk with him in person before he heard about her involvement from other sources. She also didn't want to be the one giving orders to Walker and Casey. "General Beckman, Director Graham and myself are going to speak with both you and Major Casey in the morning before we bring in the Intersect. We're supposed to contact them from a secure location at 0700 hours."
Sarah did a double take at the mention of the Intersect, her eyes wide. "How do you know about the Intersect? That's supposed to be top secret!"
"Everything will be made clear tomorrow in the debrief," Jill evaded. When Walker realized that she would get no more information from the brunette, she shook her head and set up a meeting at 0700 hours at what was supposedly Casey's address. Jill recognized the address immediately. It was next door to Ellie Bartowski's apartment. Was Chuck still living with Ellie and Awesome? Her own briefing had been short on details, but she found it hard to believe that a guy like Chuck would still be living with his sister after five years. She and Walker cordially parted ways, though Walker tried to fish for any tidbit of information from Jill, though she didn't really put any effort behind the attempt.
After Walker disappeared through the front door, Jill descended into the basement. Night was truly falling now, and she was too tired to go find a hotel. She'd kip out on one of the cots in the Castle, the name of the secret bunker laying beneath her feet. She found the hidden entrance easily enough; the book case disguising the secret door was the only piece of furniture in the entire house. There was a small button on the bottom of one of the mahogany shelves, causing the entire book case to swing smoothly open and revealing a solid steel doorway guarded by the best security the CIA could develop. A high tech scanner examined Jill's palm, retinas, and voice before the door unlocked with a loud thud.
A non-descript stairwell descended and curved out of sight. It was moments like these that almost made the job worth it. Sometimes being a spy was just so... cool. The staircase opened up into a large conference room, much larger than she and Chuck needed. An enormous table dominated the center of the room, while several gargantuan screens occupied one wall. Jill rolled her eyes after seeing her tax dollars at work. A giant tomb, larger than her head, rested on the center of the table. She pulled it towards her, reading the title. CASTLE Support Manual.Jill's eyes widened. This ridiculously sized book was the user's manual for the base? It'd take her a week of studying just to read the thing, much less commit it to memory.
She considered exploring the rest of the base, but ultimately decided to be responsible and start on her new 'required reading.' She flipped the cover open, skipped past the ten page Table of Contents, and settled into the introduction.
Ten minutes later, the young CIA agent was fast asleep.
"Agents, Major," The now familiar face of Beckman greeted at precisely 0700. Graham was slightly behind her; they must have used the General's office for this briefing. Jill was sandwiched between Agent Walker and Major Casey. They had to scrunch close together to be visible for the camera, and Jill was feeling slightly claustrophobic.
"General," Casey replied dutifully, his emotionless tone filling the small apartment.
Graham leaned in towards the camera. "We've called this meeting to discuss protection of the Intersect, as well as inform you of current events regarding Agent Larkin."
Jill couldn't help but notice Walker's slight wince at the name of her old Stanford classmate. Interesting. "What about Bryce?" the blonde asked, a slight waver in her voice.
"He escaped a high security interrogation facility two days ago. Three guards were killed during the escape, two more are still critically injured," Beckman replied, her tone cold. Walker reeled as if she'd been slapped. "He's evaded all pursuit so far."
"So you brought in extra security?" Casey asked, his eyes narrowed in irritation. "I assure you, General, we had Bartowski's protection well in hand."
"He had to land a helicopter after rescuing himself from
being kidnapped," Graham replied flatly. "He should have never been in the field in the first place."
"Director, if Chuck hadn't have been there, I wouldn't be here to have this conversation," Walker defended earnestly. "He risked his life and freedom to rescue me."
Jill's gaze hardened as she glared at the blonde. "Which is not his job, as he is the asset," she fired back, drawing stares from everyone in the room. "The moment Walker was captured, Casey should have remanded him into protective custody by any means necessary, then prepared him for emergency extraction to a secured location." The brunette focused her cold eyes on the large man, who quirked an eyebrow. "It is not the asset's responsibility to rescue the agent. We are expendable. He is not."
Casey glared at her, drawing himself to his full impressive height. "I know how to do my job," he growled, his voice low and quiet.
"Apparently not," she retorted, sounding much braver than she felt. Casey was a cold school killer who could probably murder her in a million different ways, but she refused to be intimidated.
"Enough!" Graham shouted, slamming his hand on Beckman's desk. "You are federal agents! This is a goddamn briefing! Act like it!"
"Sorry, sir," both agents and the Major chorused.
"Casey, Walker, you're being recalled," his glare silenced Walker's immediate protest. "Do whatever you have to to preserve Bartowski's cover, then take the red-eye to Wichita. Larkin's trail starts in Cypress Springs, Kansas. Track him down and kill him on sight."
"What about Chuck?" Walker asked, panic edging into her voice. "We can't leave him unprotected, especially with Bryce on the loose!"
"Agent Roberts will take over Bartowski's protection detail," Beckman stated. "You fought to keep him out of a bunker, Agent Walker. You claimed Bartowski could be trained to be an effective field agent. Agent Roberts will oversee both duties."
The blonde gaped, first at Jill, then at Beckman and Graham. Finally, she turned to Casey, looking for an ally. When the big man stared impassively back at her, she looked back at the console. "General, Chuck trusts me. His family and friends trust me. Let me protect and train him."
"Request denied, Agent Walker," the Generl said firmly, her mouth drawn in a tight line. "You have your orders."
"General, please recon-"
The door swung open, revealing a tall, gangly man with dark curly hair. He wore a white, short-sleeved button down, complete with a pocket protector and name badge. "Sorry I'm late everyone. Morgan was just..." His voice trailed off as he realized that he'd walked into a heated conversation. His gaze first rested on Walker, and something in the pit of Jill's stomach twinged when she saw the affection in his eyes. After a glance at the communication monitor, his chocolate brown eyes found hers.
"...Jill?"