Chapter 2: The Prime Directive Application

Summary: After many a relationship struggle, Sheldon and Amy finally find themselves on the same page.

A/N: Longer chapter with this update, but necessary. I know there has not been an awful lot of Shamy interaction so far in the story, but there was a reason I wanted to save it all up for its own chapter. I was aiming to post this before the season premiere taped and I'm quite pleased I made it! Hurray for deadlines!

Huge thanks to Lio for the feedback, which was more crucial than ever for me on this one. You have no idea how valuable it is to me!

As usual, I don't own TBBT or any of its characters. If I did, is this how I would write Sheldon's reunion with Amy? Good question, to be honest. For once, I don't really have an answer to that!

After nearly seven weeks of absence, the familiar three sets of triple knocks returned to her front door.

At the sound, Amy jolted in her desk chair, ripped from a deep level of concentration, and she glanced at the clock in the top corner of her screen to see it was four minutes past Sheldon's scheduled arrival time.

She barely had the chance to get up and open the door before Sheldon waltzed in, slightly breathless, and scolding his own watch. "My apologies for the delay. After we dropped Eric off, Leonard insisted we take an alternate route from the station, despite my objections that he had not checked for roadwork in the area in advance."

He spun around by the kitchen counter and crossed his arms. "Needless to say, I was right and he was wrong. And I made sure to remind him of that the whole nine minutes we spent stuck in a one-way, one-lane street, accompanied by the deafening sound of a sledgehammer."

For a reason she could not quite pinpoint, Amy felt her lips involuntarily curl into a smile at his trademark outburst about punctuality.

"It's okay. I was rather engrossed in writing a paper and had actually lost track of time until you knocked." She gestured towards the couch and made her way back to the desk. "Just give me a moment to save my work…"

Sheldon nodded and went to take his bag off his shoulder, moving towards the couch. He froze just as he was about to place it in the empty armchair, and jerked his bag back to his chest, as if the seat had been on fire.

Puzzled, he looked at the armchair, then at the couch, then back again.

After a couple of more seconds of stalling, he slung the bag back over his shoulder and quickly picked up the colorful crocheted quilt off the back of the armchair. He spun around, removed the beige checkered blanket from the back of the couch and replaced it with the quilt.

Once he neatly folded the beige blanket and laid it gently over the back of the armchair, he let out a satisfied sigh and finally put his bag down on it, sporting a content smile.

The smile fell off his lips quickly when he turned around to find Amy staring at him, her hands on her hips.

"Really, Sheldon?"

The physicist sheepishly traced the edge of the armrest with his index finger, avoiding eye contact. "I just put the quilt back where it belongs, that's all…"

Amy shook her head and turned to the kitchen to make tea. "And I just thought I'd change things around my home a little…" She shouted over her shoulder

"Well, I don't like it…" Sheldon plopped down on the couch and ran his hand over the quilt. "This is the couch throw. That is the armchair throw. It's how it's always been."

"How it's always been… in my home." Amy stressed the possessive pronoun by vigorously dunking two teabags in their respective mugs.

She carried them over to the couch and sat down in the empty spot next to Sheldon, who still avoided her eye contact. "What happened to your vow not to 'interfere with anyone's life', Sheldon?"

"I told you!" He huffed, finally looking up at her. "I'm starting on Monday…"

"Besides…" she continued, handing him his mug. ""I wasn't aware I needed your permission to change things around in my home."

Sheldon sighed deeply. A silence longer than normal stretched between them and he stared down at the mug in his hands.

After years of practice, Amy knew his sighs and his silences like the back of her hand. She knew very well what most of them meant and what she was to expect after each of them. The 'condescending sigh, the 'frustrated' sigh, the 'defeated' sigh, the 'Leonard-has-hung-the-pots-over-the-sink-on-the-wrong-hooks' sigh. And many others.

So she just kept an eye on him over the brim of her cup, knowing full well the wheels were currently in motion in his head, trying to bring up a topic he was uncomfortable with.

Her suspicions were confirmed when Sheldon opened his mouth to speak again, a slightly uncertain tone to his voice. "I have to… acknowledge… that I am much more resistant to change than the average human being."

Amy didn't even bat an eye; she just mumbled under her breath and took a sip of her tea. "I would have never guessed…"

He shot her a look of annoyance, but it was brief. His eyes lost the glare very quickly and he looked almost ashamed by his admission, his eyes darting back to his mug. "After all… it was my difficulty in adapting to change that prompted my most recent… journey."

"And it only took you seven weeks to admit it." Amy , instead, she kept her tone neutral. "I gathered as much…"

His voice changed to a fluid, lecturing quality then, as if he were regurgitating something he had already repeated to himself over and over. "I understand now that change is an inevitable part of the human condition. And that, despite my best attempts to influence others' free will, people will continue to exert change in my life, whether I like it or not."

"Change is the only constant in life, Sheldon."

"No need to cite Heraclitus on me, now, smarty pants." He scoffed at her interruption, then paused again. He sounded distressed when he resumed talking.

"Change complicates things, Amy! It was never as evident to me as during these weeks." The fingers of both his hands wrapped all the way around the mug, and tightened their grip. "There was so much uncertainty, every day, so many changes to adjust to. It was overwhelming."

He broke eye contact once again, his voice small. "Talking to you every evening was the only certain, predictable thing. And it was soothing to me."

Amy stopped drinking at that, her apparent neutrality threatened as she swallowed a sudden lump in her throat.

She didn't speak, though, and he continued on.

"It reminded me of how things were between us when we first met. Things were so much simpler back then. Before… before you changed."

As it was often the case with Sheldon, Amy didn't have time to feel moved for very long. Her shoulders sagged. "That was four years ago, of course I have changed!" she exclaimed. "You just said it yourself: change is an inevitable part of the human condition."

Sheldon puffed his chest out, his voice rising a little. "Just because I have accepted that it is part of the human condition doesn't mean I have started liking it." He said with finality.

A sudden, thick silence fell between them, and Amy rested her teacup on the coffee table with painful slowness. A slowness that made Sheldon feel inexplicably uncomfortable.

"Am I to infer…" Amy's voice was calm and seemingly devoid of any emotion. "Am I to infer, from all the evidence you've put on the table so far, that since I have changed and you don't like change… that you don't like me anymore?"

Despite her apparent stoicism, her voiced cracked slightly on the last syllable.

Sheldon almost recoiled in his seat, completely blindsided by her question. "What?! I… no! I…" he stuttered and fell silent again. He watched her take a deep breath, as if to compose herself, and his anxiety started to rise as he waited for her to speak.

When she raised her eyes to his again, instead of the anger he expected, he saw a look of determination. "Well, you know what's ironic, Sheldon?"

He figured it was a rhetoric question, but he shook his head no, just to be on the safe side.

"If you had left me where you found me… and never asked for my number, never texted me… Then never asked me out on a date. If you had listened to your mother and never rekindled our relationship back when you first had the chance to let me go, instead of working your way into my life and introducing me to your… our… friends… Then I would have never changed."

Sheldon was not sure he liked the direction the conversation was taking, but he let her finish. "So here's the irony for you, Sheldon: cause and effect. You did this." She gestured at herself. "You changed me."

His assumption confirmed, Sheldon looked down in his lap, feeling like she had just trapped his Queen in a game of chess. "Touche'…"

"So don't use that against me, this was all your doing."

"Well, now… not all of it." Sheldon feebly protested. "Maybe fifty percent…"

"Ninety-five."

"Seventy."

"Eighty."

"Fine." He grumbled in defeat.

Amy swallowed, and her voice seemed to break again. "And I'm sorry if now you don't like me anymore, but you have yourself to blame."

Upon seeing her cool demeanor crack, and her hurt seep through, a flash of guilt ran through Sheldon's eyes. But it was quickly replaced by the feeling he was most familiar with: annoyance.

"You know, Amy… being an accomplished neurobiologist does not make you a mind reader. And you of all people should know better than putting words in my mouth!" he barked at her. "I have never said I do not like you! I understand you were not graced at birth with my eidetic memory, but surely you must remember this quote… I like you for who you are, quirks and all."

It was Amy's turn to be taken aback, and Sheldon took advantage of his momentary upper hand to further his argument. "Yes. All your quirks. Including your irritating habit of biting your fingernails when you are reading, which, besides the insufferable noise it subjects me to, is one of the most unhygienic compulsions you could ever indulge in. Or how you refuse to have a clothes rotation but then become a grouch when none of your clean t-shirts match the color of the cardigan you want to wear that day. Or when you insist on writing your grocery list in your latest made up language and then get frustrated with me because I mix up bread and dish soap! And what about all these monkeys?" he waved his hands, gesturing around the room. "Staring at me from every angle of this apartment." He leaned in closer and lowered his voice to a hiss. "Even in the bathroom!"

Amy looked down at her lap. "Sheldon…"

"But not just your quirks!" He interrupted her, rolling like a freight train at full speed. "I like you changes and all. Penny and Bernadette brainwashed you into all sorts of stereotypical female malarkey, from all that wine drinking to the preposterous dates in fancy suits. Yet I still like you! Despite the fact that I am not even sure how much of this is something you genuinely enjoy or just conditioning from too much bonding with those hens."

Despite her elation at hearing those words, Amy was caught off guard by his opinion on her female friendships.

"I never considered that…" she wrinkled her forehead in contemplation. "I have to admit, there are things I do exclusively in the name of feminine peer-bonding. Like when they decided to start having that monthly online shoe-shopping evening. Or their weekly reality tv catch-up night." She frowned. "I think Rajesh enjoys it way more than I do."

Satisfied with having made his point, Sheldon nodded and sipped his beverage with a confident, smug expression. "Point Cooper."

"However…" Amy wrung her hands in her lap, knowing she was about to bring up a most delicate topic. "There are things I do genuinely want for myself… for us. And not because of… any sort of conditioning." She glanced up at Sheldon, whose expression told her he knew exactly what she was talking about. "And I know it isn't something I wanted in the past, when we first met. But now… I do. I genuinely do."

Sheldon closed his eyes and sighed his I-hate-this-inevitable-conversation sigh. Recognizing it, Amy rushed to finish before he could get a word in. "And you've been sending an awful lot of mixed signals in that area, Sheldon… In case you weren't aware." She added under her breath.

"I am." Sheldon exhaled and avoided eye contact, focusing instead on the seam of her cardigan as it wrapped around her shoulder. "What has become painstakingly obvious in recent times is that it was foolish of me to alter the paradigm of our relationship and expect things to remain as they were. I should have known that, sooner or later, you would have lured me astray."

Amy rolled her eyes. "Shel…"

"But…" It was his turn to interrupt and finish his rally. "The reason I keep sending all these 'mixed signals' " he made air-quotes. "… is that, just like with you and your… hens… I am not even sure anymore what I want because I want it and what I want because you want it from me." He paused. "It's confusing, Amy. And it's a lot of pressure. And buying time is the only way I have of figuring things out."

He finally tried to make eye contact, but she immediately looked away.

His next question was low and pained. "And I'm running out of time, now… aren't I?"

Amy's ribcage expanded a tad bit more than normal at the question, but she still didn't look at him. "We just… seem to have reached an impasse."

The statement brought a feeling of déjà vu to Sheldon, and for a moment he thought his nostrils had actually inhaled the smell of twenty-five cats. It wasn't a direct answer to his question, but it came close.

"You're not the only one who's been doing a lot of thinking during these seven weeks." Amy's voice sounded calm and logical again. "And I have to agree with you completely that our communication over these weeks has been immensely pleasurable. More so than it has been in a while…"

Sheldon looked so pleasantly surprised upon hearing her say this that she thought his face might burst, as the first genuine smile of the evening bloomed on his face.

"So…" Amy continued. "I have a proposal."

"Go on…" Sheldon encouraged her eagerly, turning to face her more directly, still smiling.

"It is clear to me that the current context of our relationship is not doing either of us any good. Therefore…" she inhaled deeply before continuing, gathering the courage to say it out loud. "I suggest we suspend all rights and obligations we are bound to as per the Relationship Agreement. For an indeterminate period."

The smile fell off Sheldon's face. "Indeterminate?"

"Yes. Indeterminate. As in a… relationship-sabbatical." She waved her hands between them. "To borrow the concept from your plans for the near future."

Sheldon eyed her carefully. "While I think your idea is brilliant, a sabbatical has a pre-determinate length, Amy. You know that. My sabbatical does in fact end in October." He fidgeted in his seat. "Unless we are talking physics, I am not particularly comfortable with the concept of indeterminacy."

"You can't put a deadline on this, Sheldon." Amy replied, firmly. "You said it yourself: you need time to sort out your life and that you won't interfere with anyone's life in the process. We just can't be in the same room 24/7 and not interfere with each other's life."

Sheldon scoffed. "Of course, not! For the tenth time, Amy, you are not moving in!"

"It was a figure of speech!" Amy shouted.

"Oh!" The physicist looked down at his hands, embarrassed.

"Prime Directive, Sheldon…" She tilted her chin at him. "No interference with the development of an alien civilization, even when well-intentioned. With a few tweaks, it's a fairly fitting concept for our situation."

"So…" Sheldon smirked at her. "You do admit that one can turn to Star Trek during times of hardship."

Amy snorted. "I have not been turning to Star Trek. I just paid attention all the times you made me watch it. Mine was merely a conceptual point to help you understand my opinion by using material you're familiar with."

The atmosphere in the room felt much lighter for a moment, but a long silence followed, Sheldon's concerns not having been entirely dissipated.

He swallowed hard before speaking.

"You do realize that an "indeterminate" amount of time can include up to…" he paused and stared at her face, clear-eyed and unmoving. "Forever?"

Amy returned his stare, her gaze unwavering. "I know."

They held each other's gaze for a long time; the first time since Sheldon had arrived at her apartment, until Amy finally cleared her throat and reached for her tea.

"You can draft a document to notify the suspension, if that makes you more comfortable than me doing it, and we can sign it before Monday so we can begin our sabbaticals." Amy suggested.

More silence followed, as Sheldon studied her for a long time. When she arched her eyebrows at him questioningly, Sheldon nodded. "Ok."

They both sipped their tea in silence for a few minutes, as a sudden, unfamiliar awareness that there was nothing more to say hung between them.

"Would you like me to drive you home?" Amy asked, talking into her mug.

Even Sheldon, for all his usual inability to understand cues, knew he had been dismissed. He shook his head and made a move to get up. "I've just returned from spending weeks riding trains across the West. I think I can manage a bus ride home if need be."

Amy also rose from her seat, wiping her hands on her thighs as she stood. "Will you bring me the draft of the… document? Or will you email it to me?"

"I think… email is probably best."

"Right."

Sheldon secured the strap of his bag across his torso and made his way to the door. He turned around to face her as they reached the threshold.

"Well… Goodnight, Amy."

"Goodnight, Sheldon."

The taller man did not make a move to leave, though, and he rubbed the sole of his shoe against the carpet. "This was… technically meant to be a Date Night." He leaned forward slightly, his voice soft. "I don't know what it is under the new parameters, but…"

"Goodnight, Sheldon." Amy repeated, decisively, taking him by surprise with her tone.

He sprung straight up like a tin soldier.

"Goodnight…" He looked down at his shoes one last time and left the apartment.

The door hadn't even been closed five seconds, when the sets of knocks came raining down on it again.

Amy stood with her back to the door and was tempted to just ignore it, but eventually reached for the doorknob to open it again. "What?"

Sheldon rushed in past her towards the bookcase and took the tambourine-playing monkey off the top of the bookcase to place it on the top shelf instead, and moved the ceramic phrenology head back in its original place on top of the bookcase.

"I'm sorry, it was driving me nuts!" He explained, apologetically.

"GOODNIGHT, SHELDON!" Amy shouted, shoving him out of the door and locking it with the latch.

With angry determination, she turned to the bookcase and stood on her tiptoes, reaching for the monkey and the ceramic bust. Just as she was about to pick them up and swap them around again, she faltered, and came back down on her feet, her hands dropping to her sides.

Staring up at the two objects, Amy shook her head and smiled. She reached for the light switch by the door instead, and as the lights dimmed in the room, so did her smile. She stood by the bookcase, in the dark, long after they had turned off.

Downstairs, at the bus stop, Sheldon was busy hugging his messenger bag to his chest and moving from one side of the bus stop to the other, desperately trying to get away from the apparently unstable, short, stocky, bleached woman with far too many tattoos who was pacing up and down the pavement, shouting obscenities over and over.

"And I thought being a hobo, riding the rails, was bad. When will this nightmare end?" He mumbled to himself.

Unfortunately for him, being the lone passenger awaiting the bus at that moment and his constant movement attracted the woman's attention.

"And who are you?!" She shouted, coming right up to his face. "You look like a weirdo! I have never seen you here!"

"I beg to differ, ma'am." Sheldon flinched and backed into the glass of the timetable. "I have taken this bus in the past, and I have never seen you here."

"Bullshit!" A spit of saliva shot out of her mouth at her exclamation, and hit Sheldon square in the chest, making him whimper and shudder.

"Although I have been away for nearly two months and usually it is my roommate who drives me, so we might have missed each other!" Sheldon let out all in one breath, closing his eyes praying a deity he didn't believe in that the bus came quickly or that the woman lost interest in him.

She kept shouting in his face. "Do you live here?!"

Sheldon shook his head, vigorously. "No, I live in Pasadena. My girlf…"

He stumbled upon the word, and his eyes snapped open. He appeared to look the woman straight in the eye, but his gaze was unfocused. It made her back away a little, looking slightly creeped out, just as the bus pulled up at the stop.

The doors opened but Sheldon did not make a move to enter. The driver leaned towards the door, gesturing at the pair whether they wanted to get on or not.

The woman stepped foot on the ladder and turned around to Sheldon again, shouting. "Aren't you getting on you, you weirdo?!"

Sheldon remained frozen in place. "No. I… I feel like walking." He replied, softly.

The vehicle's doors closed with a hiss, and the bus pulled away, leaving him standing in the dim light of the streetlight, alone.

A/N: I have to admit this was the hardest chapter I've probably ever written, and I hope I didn't disappoint you. Like I said at the beginning, I'm not sure whether this is how I would necessarily write their reunion if I was a writer for the show (although it would be one of my top choices). But, as I mentioned in the first chapter, I've wanted to write this kind of Shamy story for a year now, and the S7 finale worked just perfectly as a trigger.

I assume that, from here on, the story will diverge quite a bit from the way S8 plays out on screen, making it essentially an AU. But I have a lot of plans and I'm really looking forward to writing them out; the fun is just starting for me now! I hope it's just starting for you too.

*jingle*