Disclaimer: I do NOT own anything you recognize. They belong to their respective owners, and it SUCKS! (what I wouldn't give to own at least one of the characters...)

AN: Okay, I had this idea hit me after watching two of my favorite tv shows one after the other. You might like it, you might not. If you do, great, if not, feed the flames of my inspiration. I sometimes write my best stuff when I'm ticked off. This deals with a 'what if' scenario I thought of, and I hope you enjoy it.

The Secret Alias Conundrum

by SamiraGranger

Prologue

Light flared around them, casting the two figures in shadow. The fire that was the result of the explosion that had destroyed the building behind them roared freely as it continued to burn to the ground. Because they were in the slums of the city, no one had arrived yet to attempt to stop the flames from consuming all that it touched. Saddened eyes were averted from the sight, wincing as the sound of a beam fell to the ground from within the wreckage. Soft sobs wracked the man's body as he pleaded to the man that was with him.

"Please! There's got to be something you can do!" The criminal was kneeling on the grimy ground outside of what used to be an abandoned warehouse, on his hands and knees in front of the vigilante. "He's found out... I have to get out of here, go into hiding somewhere. Please, I need... no, I have to do this. At least so she will stay safe. I'm begging you, if not for me, do it for her. She's all that I have left in this city to care about, now that he's destroyed most of the things I kept hidden away in my various hideouts." Looking at the ground as his hat fell off of his head, the man was desperate for the help that he knew the silent vigilante could provide. Tears ran down his cheeks, falling to the floor as blood soaked through his clothes. "Please..."

Silence reigned for what felt like hours before either of them said anything. "Alright," the vigilante finally said in a gruff voice. "I'll help you. But only on the condition that, should you ever return here, you will help me if I need your input on something."

The criminal looked up at the man's words. "Of course! I'll do anything, if it keeps her safe from him," he said, astonishment showing clearly on his face. "Thank you. Truly, thank you for doing this. I promise to stay away for as long as it takes to stop that... that man, demon, whatever he is. I already have everything set up, have for years. I just need to get out of here without him noticing and then put a name on the documents..." He fell forward as something heavy hit him in the back of the head, the sound of sirens filling the air around him as he lost consciousness.

Chapter One

"...And now the kung pao chicken."

Sheldon Cooper, Leonard Hofstadter, and Rajesh Koothrappali watched as the robotic arm raised the take-out box of Chinese food from the bag and set it on the table. As Leonard and Rajesh watched the arm's movements with slight awe, Sheldon was looking at it, face blank, while Howard typed away on his laptop, already programming the arm's next set of movements. "And finally," Howard said, "my moo shu pork." When the arm reached back into the bag and pulled the said take-out box out, the three men watching clapped at the little show of technology. "There you have it, gentlemen. Our entire dinner unpacked by robot."

"And it only took twenty-eight minutes," Rajesh said, the Indian astrophysicist's accent as present as ever. While they began to grab their respective boxes of food, Howard leaned back in his chair, proud of the device that he had helped to build.

"Impressive," Sheldon remarked as he unwrapped a pair of chopsticks, "but we must be cautious."

Howard looked at him with a confused expression on his face. Although he knew he'd probably regret it, he couldn't help but ask, "Why?"

Sheldon paused what he was doing and looked at the Jewish man. "Today, it's a Chinese food retrieval robot," he explained to the aerospace engineer, as if it was obvious. "Tomorrow, it travels back in time and tries to kill Sarah Connor."

Used to this type of statement coming from the theoretical physicist, Leonard said, "I don't think that's gonna happen, Sheldon."

"No one ever does," the taller man refuted. "That's why it happens."

Suddenly, the door opened and a blonde woman walked in. "Hey," she said. "Is the food here?" As she closed the door behind her, she walked over to the robotic arm and looked it over. "Ooh, what's that?"

"That, dear lady," Howard said, leaning back with his hands across his chest, "is the Wolowitz Programmable Hand, designed for extravehicular repairs on the International Space Station."

She looked at it with a small, strained smile. Despite not understanding at least half of what the man had just said, she said, "Oh, cool."

"Ask me to pass the soy sauce." Howard was eager to show off what the robot could do again.

Penny looked at him and deadpanned, "Oh, does that come up much on the Space Station?"

"Mostly with Asian and Jewish astronauts," he replied, thinking the question was serious.

Deciding to humor the short man, Penny said, "All right, pass the soy sauce."

"Coming up." Clearing his throat, Howard leaned forward a bit and began typing away. As the seconds passed with the sound of typing filling the air, Penny, Leonard, Rajesh, and Sheldon all looked at each other as a slightly awkward silence fell over the room.

Deciding the try and break the silence, Leonard asked, "So how's work?"

"Oh, it's not bad," Penny said. "Kind of hungry."

Leonard quickly stated, "Yeah, we all are."

"Just wait," Howard said as he continued typing.

Feeling the overwhelming need to butt in, Sheldon said, "You realize, Penny, that the technology that went into this arm will one day make unskilled food servers such as yourself obsolete." Once again, he had made a jab at the fact that the young woman that lived across the hall from him and Leonard was working at the Cheesecake Factory, while the rest of the people in the room, besides Howard, who only had his masters, had doctorate degrees and worked at California Technical Institute, or CalTech, as it was more commonly referred as.

"Really?" Penny looked at him with a slightly confused look. "They're gonna make a robot that spits on your hamburger?"

As Rajesh and Leonard turned to look at Sheldon with amused glances, Sheldon turned to stare at his roommate. "I thought you broke up with her," he told the experimental physicist in a slightly irritated voice. "Why is she here?" Giving Leonard a small glare, Howard spoke up before he could respond.

"Okay, here we go," he said. "Passing the soy sauce." Hitting one final key, the robotic arm began moving.

Penny watched as it reached into the bag and pulled back out. "Hold out your hand," Howard instructed her, hand on his chin as he watched his creation in motion. Doing as told, Penny lowered her hand slightly as the robot put it's hand above her own. As it dropped a packet of sauce into her open palm, she began to chuckle.

"That's amazing," she exclaimed as she stood there, looking at the packet of soy sauce in her hand.

Sheldon scoffed. "I wouldn't say 'amazing'. At best, it's a modest leap forward from the basic technology that gave us Country Bear Jamboree." To the others, it seemed as if he honestly had no clue how rude what he had just said was to Howard.

Deciding to try and get back at the taller man, Howard said, "Hey, Sheldon?"

Sheldon looked at the engineer. "Yes?", he asked.

Howard hit a few keys on the keyboard of the laptop. The robotic hand moved, drawing the attention of the whole room as it swung around to face Sheldon. The hand raised itself into an upright position and lifted two fingers. They all stared at it, confused.

"Peace?" Sheldon was confused at what Howard was doing.

"No, not peace," Howard said, looking at the hand. "Hang on." He began typing again, trying to get the hand to do what he wanted it to do. Looking back up after he finished, he watched, smug, as one of the fingers lowered itself.

Penny and Leonard laughed a little as a look of comprehension appeared on Sheldon's face. "Ha, ha," he said, aiming a look of derision at the one male in the room that only had a master's degree. "That's not funny at all." The laughter quickly died down as Howard coughed slightly before typing again, and bringing the robotic arm into a different position.

Setting his laptop down, he got up from the chair he was sitting in and moved to sit down on the floor next to the ever-quiet Rajesh. Leonard quickly moved from sitting on the sofa to sit on the chair that Howard had just vacated, leaving the sofa open for Penny to sit in. As they all settled into their spots, all five of them grabbed a take-out box and began eating, like they seemed to always do. Passing the first couple of minutes in silence, Penny decided to ask something that was on her mind. "Does NASA know you're using that thing as a napkin holder?" Gesturing to the robotic arm that was, indeed, holding their napkins, they watched as Leonard leaned forward and grabbed one from the hand.

"Are you kidding?" Howard smiled at her, unsuccessfully trying to flirt with her, again. "They still think it's in a secure locker at JPL."

Sheldon's eyes widened a little as Penny said, "You stole it?"

Under the looks being sent his way, Howard's eyes flitted over them as he said, "Borrowed. The trick is to carry it out to your car like you own it." Just after he finished saying that, they heard the sound of a cell phone going off.

"Excuse me," Sheldon said, picking up his phone. Checking the text message he had just received, he said, "Oh, Amy's at the dry-cleaners, and she's made a very amusing pun." Clearing his throat, he read out loud what the girl had sent him. "'I don't care for perchloroethylene and I don't like glycol ether.'" Pausing, he looked around to see if anyone else had got the joke. Noticing the blank stares being sent at him, he asked, "Get it? She doesn't like glycol ether." Seeing that they still didn't understand the joke, or just didn't care for it, he explained. "Sounds like either." Doing a little inhale-laugh that he had taken to doing whenever someone had said a joke, Sheldon used his finger to type out his reply. "L-O-L."

Penny was confused. Turning to Leonard, she asked, "Who's Amy?"

Gathering up another bite in his take-out box, Leonard looked up at Penny and said, "His girlfriend."

Penny stopped eating and snapped around to look at her ex-boyfriend. In shock, she exclaimed, "Sheldon has a girlfriend?"

The man in question just looked up at this and said, "She's not my girlfriend."

Ignoring the words said by the physicist, Penny asked Leonard, "How long has this been going on?"

"Four months," Leonard replied smugly.

Shaking his head, Sheldon again stated, "She's not my girlfriend."

Still ignoring the man that they were talking about while sitting right in front of him, Penny set down her food. "Are you telling me," she said, looking at Leonard, "for the past four months I have been asking you what's new and you never thought to go with 'Sheldon has a girlfriend'?"

Beginning to become annoyed with the bickering pair, Sheldon sighed. "She's not my girlfriend," he said to seemingly deaf ears.

Penny just shushed him as she gazed at Leonard with unbelieving eyes. She asked, "How did they meet?"

Howard jumped into the conversation to explain to Penny what he and Rajesh had done, since the Indian man couldn't speak in front of the female. "Raj and I entered Sheldon's information on a dating site," he said with pride, "and it spit out Amy Farrah Fowler."

Not being able to contain her shock, Penny burst out, "Oh, my God! Sheldon and Amy."

"Or as we call them," Howard said, "Shamy."

Penny squealed in delight, clasping her hands together in joy. "Shamy," she said. "I am so digging the Shamy."

Unable to handle the conversation a moment longer, Sheldon put his food down and stood up from what everyone called 'Sheldon's Spot'. "All right, everyone pay attention," he said, annoyance lacing his voice. "Yes, I have a friend named Amy Farrah Fowler. Yes, she is female. Yes, we communicate on a daily basis, but no, she is not my girlfriend." And I should know, he thought to himself. I already have a girlfriend.

Walking away from what he thought was the end of the conversation, he was stopped as Penny asked, "Okay, well, what do you communicate about?"

Looking back at the blonde, he said, "Well, my work in physics, her work on neurobiology, and most recently, the possibility of our having a child together." Although that's mostly her idea, and not mine. Keeping that last bit to himself, again, he walked behind the sofa as Penny spat out her drink at what he had said last.

As Sheldon walked over to the refrigerator to grab something to drink, Howard typed something onto his laptop. "Thank you," Penny said as she accepted a napkin from the robotic arm that had just extended out to her.

Leonard turned around in his chair to stare at his roommate as Sheldon got out the bottle of apple juice. "Wait a minute," Leonard said as he stared dumbfounded at the theoretical physicist, "a child? You never see this girl. You just e-mail and text and Twitter. Now you're considering having a baby?"

Sheldon looked at them as he mentally sighed. Is this conversation never going to end? Keeping the thought to himself, as usual, he said, "Amy pointed out that between the two of us, our genetic material has the potential of producing the first in a line of intellectually superior, benign overlords to guide humanity to a brighter tomorrow." Turning around to grab a glass to put the juice in, he hid the look of disgust that crossed his face at the thought of what Amy had suggested. I told her it would be a bad idea, he thought. And now look at what is happening. I knew I should have told them I had a girlfriend already when I had the chance.

He heard as Howard whispered to Raj, "I'm guessing that future historians will condemn us for not taking this opportunity to kill Sheldon." Knowing that Raj was nodding in agreement, Sheldon mentally sneered at the idea that the two of them could possibly come close to killing him.

"Okay," Penny said standing up, "I have a question."

Sheldon looked up from pouring his drink and said, "Yes, Penny."

The girl walked over to him and said, "You don't even like people touching you. How are you gonna have sex?"

Looking up sharply at the highly unexpected question as he finished putting the cap back on the bottle of apple juice, Sheldon looked at Penny, being careful to make his expression blank. "Why on Earth would we have sex?", he asked, trying to keep what he truly felt about the idea from showing in his face. Turning away from the girl as he put the juice back in the fridge, he heard something that nearly made his blood boil in anger and indignity.

"Oh honey," Penny said, "did your mom not have the talk with you? You know, when your private parts started growing?"

Rage burned within him as he had to look away from his neighbor to keep himself from giving in to the urge to slap her. I never even knew my mother! My stupid and abusive father blamed me for her death, he thought, trying to keep his temper under control. "I'm quite aware of the way humans usually reproduce," he informed Penny, "which is messy, unsanitary, and, based on living next to you for three years, involves loud and unnecessary appeals to a deity." Not that I would mind doing so, he thought as he stared at her, thinking of his missing girlfriend.

"Oh, God," Penny groaned, embarrassed.

"Yes, exactly." Walking passed the stunned blonde with his drink, he stopped at the entrance of the hallway that led to his and Leonard's bedrooms. "Consequently, if Amy and I choose to bring new life into this world," he said, seeing a semi-perfect opportunity to further embarrass the blonde girl, "it will be accomplished clinically, with fertility experts in a lab with petri dishes." Turning back to Penny, he had to hide a smirk as he carefully chose his next words. "Which reminds me, you have broad hips and a certain corn-fed vigor. Is your womb available for rental?"

Giving her a look that was sure to make her think that he was being serious, he was distracted when Leonard said, "Still digging the Shamy?" Looking at his roommate, he mentally rolled his eyes.

"Look, Sheldon," Penny said, getting Sheldon's attention back on her, "before you race off to the fertility clinic, you might want to think about, uh gee, I don't know, maybe actually spending some time with her."

Deciding to play the socially-ignorant fool, yet again, Sheldon said, "You mean dating?"

Penny smiled as she nodded her head. "Yeah," she said.

"I can't date Amy," he told her.

"Why not?"

Eyes widening at having to say it again, Sheldon mentally groaned. "She's not my girlfriend." Seeing that Penny was beginning to get exasperated with where this was going, he thought, I would never willingly cheat on the girlfriend I already have.

"Okay, look," Penny finally said, completely missing his hidden point, "don't think of it as dating a girlfriend. Think of it as, uh, getting to know the future mother of your child."

Putting on a look of realization, Sheldon stated, "Oh. I hadn't considered that. I suppose she will have to have access to our progeny." Looking at Penny with raised eyebrows, he asked, "And you don't think I can achieve the required intimacy via text messaging?"

"Probably not," she told him.

"Huh," he said. "It would appear as if the phone companies have been lying to me." Making his way back to his seat, he sat down and picked up his food. And it looks like I'll have to do something drastic to stop them from continuing the line of thought that they have taken, he thought as he began to eat his food again, his previously good mood thoroughly ruined.

~?~?~?~?~?~?~?~

Closing the door to his bedroom about an hour and a half later, Sheldon's back slid down the door until he was sitting on the floor. Taking his contacts out of his eyes before he did anything else, he put the colored pieces of soft plastic back in their case and rubbed his eyes slightly to get used to not having the blue discs in them. Running a hand through his short brown hair, he let his eyes wander around the room. "What am I going to do about this?", he whispered to himself, making sure to keep his voice quiet to prevent Leonard from hearing him. "I... If Amy does want to be my... my girlfriend, I can't allow myself to get her hopes up."

His green eyes landed on the door to his closet. It's been at least seven years since I last saw her, he thought as he slowly stood up. Does she even still care about me? Do I even have the right to call her my girlfriend after pretty much abandoning her the way I was forced to? I didn't even have a chance to leave her a message about what was happening. Has she moved on with her life in my absence? With those questions and other similar ones floating around his head, he walked over to his closet and opened it. Looking at all the shirts he had hanging within the small space, he pushed them all to the sides, making an empty space in the middle of the shirts that allowed him to see the back wall of the closet.

Reaching a shaking hand out to touch the back of the small space, he felt the hidden panel that he had installed in the closet when he first moved into the building being pushed in slightly. Moving the panel to the side to reveal what was hidden behind it, he felt his whole body begin to shake in fear as he stared at the complete, immaculately folded outfit that was laying within the hidden compartment. Picking up the hat that was laying on top of the pile of clothes and setting it to the side, he gulped at the sight of the phone that had been sitting underneath the hat ever since he had arrived in Pasadena, California. Slowly, he picked the prepaid phone up and set the hat back down on top of the outfit.

Turning the little flip-phone over in his hands, he let out a shuddering breath at what he was about to do. This could very well be the one mistake that makes it where he can find me, if he's still searching for me, that is, he thought. But I don't care anymore. I've been hiding for too long as it is. I don't want to hide away for the rest of my life, I refuse to continue to pretend to be someone I'm not. Making a decision that he hoped he wouldn't regret later on, he opened the phone and turned it on after plugging it onto a charger. Scrolling through the contacts list after a few minutes, he found the number he needed and hit the call button.

Holding the phone to his ear, he listened as the phone rang, waiting for the person on the other end to pick up. "Hello?", he heard in his ear.

Taking a deep, calming breath, he said, "Hey, Missy. It's... It's me. I'm sorry to be calling out of the blue like this, but could I possibly... Maybe... Talk to her? I already know that she's there, I've been keeping track of where she is these past few years. I... It's time for me to tell her the truth. I can't keep this up for much longer. I feel like I'm about to be lost inside this... this monster I've created."

He heard nothing as he waited nervously for a response. "S-sure, you can talk to her," Missy said. "Just... Just let me get her in here right fast, okay?"

Sheldon sighed as anxiety filled him. "Thank you, Missy," he said into the phone. "I really appreciate this. I just hope she understands."

"So do I... Shelly," Missy said before the sound of her handing the phone to someone echoed in his ear.

"Hello?" A light, feminine voice spoke into his ear in a soft soprano. "Who is this? Why did my sister call you 'Shelly'?"

A small smile appeared on his face as a single tear ran down his cheek. "Hello, my dear," he said softly into his phone. "It's so good to hear your voice again." Hearing the new voice speaking into the phone, trying to understand who he was, he couldn't help but let out a quiet sob. "I miss you, so much. Please, I... I am so sorry. I didn't mean to disappear on you like that. Please, allow me to explain myself. I beg of you, little sphinx, hear me out. I'll explain everything to the best of my abilities. I just need you to be willing to hear what I have to say."

The other end of the line was silent for several minutes, almost making him think that the girl had hung up on him. His heart began to feel heavy, the idea that he wouldn't have the chance to redeem himself to the one person that mattered the most making him feel nauseous. "A-alright," he heard the feminine voice say finally. "I'll let you explain yourself. Then I'll decide whether or not I want you to contact me again. The way you left... It hurt, a lot. You do realize that, right?"

"Thank you," he muttered into the phone, relief flooding through him. "I just hope you can forgive me for what I did. I had been forced into a corner, and I couldn't think of any alternate choice." With that said, he laid back on his bed, getting ready for a long night of explaining himself over the phone to the only person that could help him return to who he truly was.