Disclaimer: I do not own The Big Bang Theory or any of its characters. If I did Sheldon/Penny would be so on. I do however take responsibility for any and all science errors.

AN: This is the much requested sequel to The Cooper-Fowler Relationship Fallacy. This story picks up two weeks later. I highly recommend reading that story first. Unlike the previous story which was conceived as a one-shot this story will be multi-chapter.

AN: Spoilers up through all of season 3. Events from season 4 may work their way in as well so if you aren't up to date then you may be spoiled. This chapter discusses the new Star Trek movie extensively so there are spoilers for that as well.

The Emotional Attachment Determination

Chapter 1: The Best Friend Protocol

"But I don't want to watch the new Star Trek movie." Sheldon stated with a hint of a whine creeping into his voice.

"Well too bad." Leonard said. "We've all agreed on it."

"Why don't you want to watch it?" Penny asked ignoring Raj and Howard waving their arms around wildly trying to signal her to stop talking. "I thought you loved Star Trek and this one is all about Spock."

"If by 'all about Spock' you mean this is the movie that complete destroys his character. Do they really expect us to believe that an advanced mind such as his would choose to forgo his Vulcan reason in favor of his baser human side?" Sheldon asked, his voice full of derision.

"I'm not sure what show you were watching but that was the whole point of his character development before this movie." Howard said with a sigh.

"I acknowledge that in the original continuity his character grew to embrace certain aspects of his human side such as friendship but certainly nothing so...so common as a libidinous relationship with Uhura." Sheldon sat up straighter. "Even the presence of Leonard Nimoy, reprising his role as the Spock from the original timeline, does nothing to ameliorate the writers' atrocious pandering to the lowest common denominators in the audience by introducing a frivolous romantic subplot."

"I thought it was sweet." Penny said grinning broadly at Sheldon from her seat in the armchair.

"You would." Sheldon said shaking his head. "Which proves my point."

"What was your point again?" She asked innocently.

Sheldon opened his mouth to answer her when he realized that her question had not been asked out of a genuine desire to understand his viewpoint. "It is obvious that you lack the necessary background to fully understand my argument. Suffice it to say that you are the intended audience for this movie and not me."

Penny looked over at Leonard. "Why did that feel like an insult?"

"Because it was one," he said hitting play.

Instead of paying attention to the movie, Sheldon once again turned his mind to the Penny Problem, as he had begun to refer to his realization of their changing relationship. He had been mildly uncomfortable in her presence ever since the night two weeks ago when he had come to the conclusion that she was his best friend. The whole situation seemed horribly unresolved and the uncertainty disturbed his sense of order. He didn't have any sort of guidelines to help him navigate the situation the way he did with Leonard.

The roommate contract had proved invaluable, outlining the necessary steps he needed to take to maintain his side of their friendship. It specified everything from the frequency he should ask about Leonard's day and the appropriate etiquette for dealing with Leonard's sexual partners to the obligations should one of them develop time travel. The more Sheldon thought about it the more a new contract seemed like a good idea. Not that he expected Penny to develop time travel. Of course the likelihood that Leonard would do enough original research to manage it was also laughable.

Sheldon hiccupped a laugh at the thought of Leonard actually making any significant contribution to science. He only realized the poor timing of his amusement when four sets of eyes turned to look at him disapprovingly. Glancing at the screen he realized that Spock's mother had just died.

Deciding that explaining the joke would be a pointless endeavor, Sheldon got up from his seat and moved to his desk. Now that he had determined that a contract would be the perfect method of managing his friendship with Penny, he wanted to get started immediately.


Penny had just gotten out of the shower when she heard the first three knocks on her door. She quickly threw on her new pink, flamingo print pajama pants and a lime green camisole and made it to the door just in time for the third set of knocks.

"Penny." She heard from the other side of the door.

Penny threw open the door to find Sheldon holding a large stack of papers. "Yes?"

"Here," He said holding the papers in her direction. "Please look these over and fill in the blanks."

"Fill in the blanks?" Penny asked looking suspiciously at the papers in his hand. "Is this another friendship test?"

"No." Sheldon said. "The status of our friendship is not in doubt. This is merely a contract that outlines the parameters of our social interactions."

"You want me to sign a contract?" Penny asked in disbelief, taking a step further away from the papers he was holding in her direction.

"This is merely a first draft. There are several areas that I have left blank for you to outline your requirements. I also expect that there will be some points you will wish to negotiate before signing." Sheldon waved the papers in her direction but she clasped her hands behind her back.

"Sheldon," Penny said, completely confused. "Why do you want me to sign a contract?"

"Everything is explained in the preamble." Sheldon said avoiding her eyes.

He looked so uncharacteristically self conscious that she grabbed the papers from him. "I'll look at it but don't expect me to sign anything."

A look of relief passed over his face as he turned and walked back to his apartment without so much as a goodbye. Irritated at the lack of consideration, she leaned out of her door and called after him. "Goodnight, Sheldon."

"Goodnight, Penny." He responded as he closed his door.

Shaking her head at the crazy that was Sheldon Cooper, Penny closed the door and set the papers on her coffee table. She returned to the bathroom and as she brushed her teeth she couldn't help but think of Sheldon. She didn't think that she would ever get used to having him as a neighbor. For someone who was so set in his routines he sure had a knack for shaking her out of her's. No one else in her life had the ability to irritate her so badly that she wanted to go junior rodeo on them one minute and then turn around and make her so happy she could cry with just a hug the next. Not that he gave out many hugs.

Penny smiled as she remembered the first hug he had ever given her. He had been so happy about that silly napkin that she had given him two years ago that he hadn't been able to contain himself. She was fairly certain that it had been the first time he had spontaneously hugged anyone. Penny had been so touched by the uncharacteristic gesture that she had nearly cried. After all, she knew he wouldn't have hugged her unless he really wanted to. That was the thing about Sheldon, you always knew exactly what he thought. Whether you wanted to or not.

Once she was done, she retrieved the papers and crawled into bed to look at them. Penny frowned, thinking that it was a bit strange that he didn't just come out and tell her what the papers were all about. It was almost like he was nervous which wasn't like Sheldon. She glanced down at the first page and began to read.

I, Dr. Sheldon Lee Cooper, upon the realization of a state of friendship that has progressed to a level above all others do hereby outline the proper protocol to maintain said friendship.

Penny's mouth dropped open. She quickly skimmed the rest of the document, completely skipping the sections that discussed the acquisition of super powers and the development of time travel. True to his word he had left several places for her to describe her needs. There was a place for her to indicate how often he should ask about her day and room for her to list any topics that she considered off limits to conversation. There was even a space for her to fill in her medical history.

For one crazy moment, Penny was almost tempted to go along with the contract just so that she could veto a few topics of conversation. She was pretty certain that Leonard, Howard, and Raj wouldn't hesitate to fill up that section. But as tempting as it was to prevent Sheldon from ever calculating the number of men she had slept with again, she couldn't let him think that a contract could ever apply to a friendship.

She looked back at the first line. After reading it several times she was convinced that he was trying to tell her that she was his best friend. As awkward a gesture as it was it was kind of sweet and he was trying to take her feelings into account in his own completely inept way. She remembered Leonard telling her all about the roommate contract he had signed when he first met Sheldon. It hadn't sounded like Sheldon had left any room for negotiation in that one, much to Leonard's current dismay.

If he had given this to her two years ago she would have probably been offended or at least annoyed but she knew Sheldon well enough by now to know that he hadn't meant any offense when he had included an entire section about her dating habits and which nights of the week she could go out. She was able to interpret the Sheldon-speak and realize that what he really wanted to do was make sure that she still had time for him.

Penny sighed, putting the papers on her nightstand and turning out the light. This whole situation was very confusing. She had so many questions.

When had Sheldon decided that she was his best friend? Wasn't Leonard his best friend? What was she going to say to him tomorrow? And perhaps most importantly, what place did Sheldon hold in her life?

Burrowing under her covers she began to think about her friendships. She had always been popular in high school but she wasn't really very close to any of her old school friends now. Most of them were back in Nebraska dealing with mortgages, children, and in too many cases messy divorces. Their lives were worlds apart from her own. When she had first moved to California she had made a slew of new friends to go out to clubs with and watch football games with but none of those people were particularly close friends. If she were completely honest with herself, the only people that she knew she could really count on were Sheldon, Leonard, Raj, and even Howard.

There were a few girls at work that had potential but she had spent so much time with the guys since she had started dating Leonard that she hadn't spent much time with anyone else. She liked the way she could be herself around them without any expectations. But out of the four of them she was closest to Leonard and Sheldon.

She rolled over and stared at the light from the nightlight she kept on in her bathroom. As much as she cared for Leonard their friendship had always been strained. Whether it was his awkward insecurities or her self consciousness about her lack of education they were always afraid of letting the other down. They had constantly waffled between romance and friendship in a way that never let either relationship bloom the way it should.

But with Sheldon it was different. He might treat her like she was stupid sometimes but he treated everyone that way so it didn't hurt her feelings. He might be rude but he was also always there for her. She couldn't think of a single time that she asked for his help that he didn't give it to her. He had even driven her to the hospital despite being terrified of driving. And she knew that he would always be there. He had proven that when he had snuck around behind Leonard's back just to eat spaghetti with her.

Sheldon also needed her and Penny would be lying to herself if she said she didn't like that. Sure he sometimes frustrated her so badly that she wanted to scream but it felt good to be needed. This Beautiful Mind-type genius needed her to help him pick out suits and figure out first dates. Over the years he had grown to trust her when it came to social situations.

They actually had a give and take relationship. He never treated her like a sex object like the other boys did and she never turned him away like everyone else did.

"Well damn!" Penny exclaimed, sitting up. "Sheldon Cooper just might be my best friend."

When had that happened?