There was utter silence in the apartment, apart from the forlorn wails of baby Stephen. He rooted frantically at the front of Penny's shirt, stymied by the unfamiliar fabric barrier. Sheldon looked at her, and some wordless communication seemed to pass between them. He placed a hand on the small of her back and guided her to his old room for some privacy to nurse Stephen. He returned to face his friends alone. Sheldon cleared his throat nervously. He and Penny had discussed what it might be like when they got home, but in none of those scenarios was he left by himself to explain their absence and the sudden appearance of an infant.
"Let me begin by asking that you hold your questions until I am done speaking," Sheldon began, his nervousness making him sound rather pompous.
"Oh, for heaven's sakes, Sheldon, we're not one of your undergrad classes," snapped Bernadette. Her comment elicited a few nervous chuckles, but the atmosphere in the room was still tense.
"I recognize that, and I didn't mean to imply that you were. I simply don't wish to relate my story more than once."
"Dude, we're all ears; now tell us," Raj begged.
"My story began the night of March 18th. Penny was driving me to Stuart's comic book store, as Leonard, Howard and Raj had elected to go see a movie that evening without me. The next thing I remember after that is regaining consciousness in a visually peculiar room. Penny was there as well, but we were missing all of our personal effects."
"All of them? Wait, wait, wait… do you mean you were naked? Did you see Penny naked?" cut in Howard eagerly, earning him a glare from Sheldon and a punch on the arm from his wife.
Sheldon's cheeks tinged with color, but he answered with as much dignity as he could. "I believe that is what I implied when I said all of our belongings were missing."
His audience listened, spellbound, as he described how they had explored the purple room, and how Penny had discovered the scar on his head. Everyone gasped as Sheldon turned his head and parted his hair so they could all see the nearly-healed line for themselves.
After he told them about the strange telepathic communication, and how he and Penny had both been tampered with, there was little left to tell… or rather, little that he wanted to share. Then came the shocking news of the alien's experiments with their genetic material.
"And that's where the baby came from?" Bernadette interrupted. "I was doing the math in my head, and I don't think there's any way Penny could've been pregnant before she disappeared. That baby still looks pretty young. She would've had to be about five or six months along, and I think we would have noticed if that had been the case."
Sheldon quietly noted that her words confirmed his suspicion of time travel. For him and Penny, it seemed that they had been away for almost a year, but to their friends, they had only been gone for five or six months.
Leonard scowled as he answered, "Trust me, Penny's my girlfriend; there's no possible way I could have missed her being six months pregnant."
"So you are certain that the infant is the result of a combination of your DNA and Penny's?" Amy asked Sheldon in a flat voice.
"I'm so sorry, Amy. It's complicated, I know," came Penny's voice from the back hallway as she rejoined the group. She had filched another of Sheldon's t-shirts to replace her damp one, and the physicist felt a surge of desire to see her wearing his clothing. It made him feel as if she was his, as if she belonged with him. He quickly averted his eyes before his expression betrayed his feelings.
Penny continued, "We must have been the only humans they picked up. Stephen looks a lot like Sheldon, and I feel like he is my child. Before they brought us back, the one alien told us he could… eliminate Stephen if we didn't want to keep him. I told them there was no way in hell they were laying a finger on my baby." She took a deep breath. "I don't know how things will work out, but I have a child now, and I have to do what's best for him."
"So you're really backing Sheldon's crazy alien abduction story?" Leonard asked incredulously.
Penny lost control of her fragile emotions. "Story? Story? Do you think we're making this up? What the hell is wrong with you, Leonard? Do you really think either one of us wanted to just leave our entire lives behind, scaring our family and friends to death? Do you think we chose to be kidnapped? To be locked up in a cage and experimented on like lab rats? To have everything I knew ripped away from me with no hope of ever seeing anyone I loved—or hell, even my planet—ever again?" She was simultaneously glaring furiously at him and fighting back tears.
"I—I didn't say that," Leonard faltered.
Then, to everyone's surprise, Penny drew in a deep breath and apologized. "I'm sorry, Leonard," she said shakily. "I'm angry, but it's about what happened to me and Sheldon, not because of anything you did. I'm still trying to sort everything out in my head, and I realize I've had a lot more time to deal with it than you've had."
"Uh, that's okay, I guess," Leonard replied, giving her his best placating smile with his head tilted to the side.
"Well, I think I speak for everybody when I say, we're just so happy you're back," Raj said joyously. He walked up to Penny and gave her a huge hug. Penny returned his embrace with tears in her eyes. "Thank you," she whispered. Suddenly the tension melted away, and everyone was hugging Penny and Sheldon too, despite his obvious discomfort with physical displays of affection.
Howard and Bernadette saw that there were private conversations to be had, so they made their excuses before it got too late in the evening. Raj got the hint as well from a not-so-subtle elbow in the ribs from Bernadette and a jerk of her head towards the door. Leonard went to help Penny improvise a bed for Stephen, leaving Sheldon alone with Amy. He threw a panicked glance at Penny as she left. She met his gaze steadily, and gave him a small nod of encouragement. He turned his attention back to Amy, who was regarding him with an inscrutable expression.
"Would you care to take a walk, Amy?" he asked.
"I think that is advisable," she agreed. Opening the apartment door, she led the way, and the two of them stepped out into the night together.
Sheldon and Amy were silent as they walked down the four flights of stairs and through the front door of the apartment building. As they walked down Los Robles, Amy gathered her courage and spoke up.
"You seem different, Sheldon," she ventured hesitantly.
"I suppose being abducted by aliens would be considered by most a life-changing event," he replied.
"True, but you seem more… relaxed somehow." She stopped and put a hand on his arm. He looked slightly uncomfortable but merely returned her gaze expectantly.
Her lips compressed into a thin line. Somehow, the fact that he wasn't freaking out because she was touching his arm only made matters worse. "I can't help but notice the way that you and Penny were looking at each other, Sheldon," she accused in a peevish tone of voice.
"And which way was that?" he asked warily.
"You look at her in a way you never looked at me. Your eyes follow her wherever she goes. And the look on your face is very… soft. Sheldon, are you in love with Penny?" she demanded abruptly.
"No, of course not," he scoffed, but the expression in his eyes didn't match the tone in his voice. He wasn't directly lying, but Amy could tell that something was up.
"All right, then tell me that nothing inappropriate happened between the two of you," Amy ordered in a reproachful tone. Sheldon looked away, but he couldn't hide the facial tics which signaled his discomfort. Amy clapped a hand over her mouth and stood staring at him for a long time. Two tears streaked down her cheeks. Finally, she sat down on a nearby bench and said in a low voice, "Tell me what happened, Sheldon. You owe me that much."
He was torn between a sense of obligation to Amy and his promise to Penny. But he knew Amy had already guessed some of it. Mentally reminding himself of his resolution to stop living in fear, Sheldon sat down on the bench next to Amy and began to tell her a carefully sanitized version of how he had ended up in this strange, undefined relationship with Penny. He regretted knowing he had hurt Amy's feelings. After all, he did care about her, just not in the way she had always hoped.
After Sheldon had finished speaking, Amy was silent for several long minutes. Finally, she said, "Sheldon, I have something to say, and I want you to promise that you will hear me out without interruption or questions." Sheldon nodded, curious but unsure.
"I was wrong about something, Sheldon," Amy began. "When we first met, you only wanted to be friends, and I did too. I was the one who changed. I wanted our relationship to go beyond friendship. So I pressured you and manipulated you. I made you feel ashamed and guilty for being yourself. I took advantage of my knowledge of behavioral conditioning to make you do what I wanted. I tore down your sense of self to remake you into my boyfriend. At first, this course of action seemed perfectly logical and rational to me. But as I got to know Penny and Bernadette, I began to realize that you shouldn't treat your friends like a lab experiment. I felt bad about what I was doing, but I just couldn't stop. I interpreted the slightest gestures from you as proof that you loved me."
Sheldon's eyes bulged at her mention of the word "love", but he kept his mouth shut as promised.
Amy continued, "Tonight, I've seen you look at Penny like a hungry lion watching a gazelle on the African veldt. It's made me realize that what I had with you was a poor and rather pathetic imitation of a real relationship."
She took a deep breath and met his gaze, her eyes shimmering with unshed tears. "You don't owe me an apology, Sheldon; I owe you one. I'm sorry for trying to force you to be the boyfriend I wanted you to be. I hope we can be friends again someday."
They talked for a while longer. Sheldon had neither accepted Amy's apology nor tried to excuse his feelings for Penny, mostly because he had no idea what he should say. He found himself wistfully yearning for Penny to be there with her supernatural empathy. With her, he never felt the need to explain how he felt. The tension between him and Amy lessened as she changed the subject and started talking about her latest research project. He listened and asked a few pertinent questions. Then she told him about how their whole group had been meeting weekly to discuss their search efforts to find him and Penny. She had become much closer to both Bernadette and Raj, and said she hoped the weekly get-togethers would continue even though he and Penny were back.
For once, Sheldon said little, but allowed Amy to speak. He had always valued their friendship. Learning that he had developed romantic feelings for Penny had to be difficult for her. The whole situation was very trying. Despite his feelings for Penny, neither of them were certain their bond would withstand the pressures of real life. That was why she had insisted that they spend time apart. Specifically, he knew that Penny doubted whether he could accept the turmoil that would come if they announced they were together. She knew how much he loved his solitude and routine. It was almost like she was trying to push him back into it. The situation bore a strong resemblance to the way she used to encourage his relationship with Amy. He knew Penny always wanted what she thought was best for him, but in this instance, he was convinced she was wrong. He would give it some time and allow her to think he had made a rational decision. But the truth was that he didn't know how he could live without her. If she wanted to call it co-dependent, he would accept that. He only knew how meaningless his life would be without Penny.
A pause in the background noise made him realize that Amy had asked him a question. Quickly, he reviewed her last words. He had allowed his mind to wander, but his eidetic memory enabled him to respond appropriately. He was still fond of Amy, but he realized he could never have the romantic relationship with her that she wanted. In time, he hoped they could return to the easy camaraderie they had once enjoyed.