Disclaimer: Same as before - Alias does not belong to me, so please don't sue.

A/N: Hi again. I know I just did Chapter One last night, but I have this one sitting here and have to upload it cuz... Well, cuz I want to. One thing I forgot to add: Project Prodigy is a term I got out of the Official Alias Magazine. I have no idea if that's in reference to the black folder or something else, but though I'd use it anyway. Okay, that's all for now.

It took three days before I went back to Los Angeles. I didn't know what to do. Go back to the CIA – I had figured that much out. If I didn't, it wasn't like I had anywhere else to go. Sure, I could disappear, but where would that leave me? It would be just like when I had come back from my missing time – my time with the Covenant as Julia Thorne. I'd have no job, no friends, no place to live…

So, finally, I flew back.

I didn't say a word to anyone as I walked into the Rotunda, going straight back to Dixon's office. He was inside, alone, and I closed the door behind me. He seemed surprised to see me.

"Sydney. Everyone was worried about you," he said, standing and coming around in front of his desk. "Have a seat."

"Dixon, there's something I have to tell you," I stated. I didn't sit down – everything I needed to tell him was… I wouldn't be able to sit still enough to stay there, and would constantly be getting up and down.

"All right," he said, nodding. "Go ahead."

"When I left here, after they took Vaughn to the hospital… I went to Palermo to look for Lauren," I began. "I know, it was against protocol, but I felt that she needed to pay for what she did. And, I wanted to see about the Rambaldi device – I needed to know if it was actually there. If Sloane was there looking for it, with Nadia. In Palermo, I ran into my mother's sister, Katya Derevko."

"Yes, Agent Vaughn mentioned that she was the one that stabbed him," Dixon replied with a small nod. He was leaning back against his desk, as I paced the room.

"Right. I tranquilized her, and tried to take Lauren out. One of the workers got in the way – I shot him in the arm. We fought… It was dark and there weren't many other people there. Most of them had already gone for the evening, or run off when I fired the shot.

"Lauren started to say something. About… Being pawns involved in some greater scheme. Of course, I thought it might be a ploy – something to buy time. She told me that if I killed her, I would never know the truth. She told me that she knew who was controlling her, but that I would never know unless I listened to her.

"I got distracted. She won the fight, but Vaughn showed up at the last minute. I guess Weiss told him where I'd gone and he came to make sure that I was safe from Katya," I sighed a little, shaking my head. "Vaughn shot Lauren. She stumbled, but regained her balance and tried to attack us again. He shot here, probably five… Six times. She fell into the hole at the dig site. But, before she did, she told me there was a bank in Wittenberg. A safety deposit box, number 1062, that would tell me what I needed to know."

"So you went there… To Wittenberg?" Dixon asked. He looked concerned, and also a bit confused about what I was telling him.

"I did," I answered. "And, what I found there…" I paused to take a breath. "There was a black folder inside the bank vault. I was left alone in the room, so I broke into the box and removed the folder. Which was locked with an electromagnetic keypad and code. I short-circuited the keypad, and removed an official CIA briefing folder. It had the seal on it and everything.

"Inside were several black sheets of paper. They could only be read with an ultraviolet light that I had with the rest of my gear. On the pages… It was detailed information about a CIA-sanctioned project referred to as "Project Prodigy".

"As far as I can figure… Project Prodigy is a project that was put together by my father. Begun the day I was born. The rest of the file… Details everything I've been through since I was a child. It seems that most of the preliminary work was leading up to my training under the Project Christmas program – the program my father developed for the CIA when I was six years old. The Intel that my mother came here to steal from him.

"But, as I looked at more of the information, it appears that it's not that simple. I was never trained under the Project Christmas program. At least, not directly. This Project Prodigy… It seems that my father was developing a project, funded and fully sanctioned by the CIA… To train me to find and kill my mother."

"What?" Dixon asked, standing up fully now and looking at me in shock.

"According to this project, my recruitment into SD-6, becoming a double agent for the CIA, destroying the Alliance… Possibly even my abduction by The Covenant… Was the work of my father and some of the leading members of the Central Intelligence Agency."

"Your father began this project on the day you were born… He didn't know that your mother was KGB until years later. How could he have known that you were to be programmed to that end?"

"That's the thing – I don't think he did," I answered. "But… Either he did know, and that was why he programmed me under this Project Prodigy… Or he began to program me anyway, thinking… I don't know, that I could be brought into the CIA as some kind of a super agent, and then changed the aim of his project once he knew my mother's true alliance." I sighed, shaking my head. Finally, I stepped further into the room and sank into a sitting position on one of the couches in his office, dropping my head into my hands. "And he knows that I know."

"He found you in Wittenberg?" Dixon asked. I nodded a little.

"I have no idea how," I answered. "Just… I heard his voice just a little while after I got there. He told me that I was never supposed to find the files." I shook my head again, looking off to the side of the room. Finally, I looked back at Dixon. "Has he been controlling me from minute one? Has everything I've done for the last twelve years of my life been nothing but a lie?"

"Sydney…" Dixon came over beside me, taking a seat as well and sighing deeply with sympathy. "Even if all of this information is true – which, since it came from Lauren Reed, you cannot possibly be sure of that – there's no way to be certain that any of this was really your father's intention. You certainly can't believe that your abduction was his fault."

"How else would it have happened?" I asked, standing again. There were tears in my eyes. I wanted to believe what Dixon was saying – that none of this was really his fault, that didn't mean for any of this to happen. But… The more I thought about it – how the Covenant had known what would hurt me the most, what to show me, who to threaten to try and brainwash me…

They knew where I lived. They knew about Francie, they knew everything.

He had something to do with it.

"The Covenant was listed as a 'rising threat' on the terrorist list the day I disappeared," I started. "They knew about Francie being doubled – they knew about Allison Doren. She didn't work for them at the time. They knew to find her body – her real body and plant it at the scene before they set the fire. They abducted me.

"They knew what would hurt me the most.

"Lauren worked for the Covenant. They asked her to come to Los Angeles, to start a career with the NSC. That was why she married Vaughn. To get information from him, sure, but also because it would affect me to see him like that, should I ever escape their 'control'," I continued, just stating my thoughts as they occurred to me. Dixon was looking at the crazed look in my eyes, worried, but I couldn't stop talking.

"The only person that would have known all these things was my father. I mean, sure, Sark knew but he didn't work for the Covenant. He worked for Sloane…" Suddenly, I stopped.

Sloane.

I swallowed thickly, and sat back down, this time on Dixon's desk. And, this time, I didn't do it because I was overwhelmed with emotion and tired of pacing.

I did it before I fainted.

"Sloane," I stated again. I took a moment to catch my breath, and then looked up at Dixon seriously. "Sloane knew all those things. He was the one that gave me the key, leading to the apartment in Rome. Julia Thorne's apartment. He gave me the key, that led me to the desert. Lazarey's hand. That led me to him, that gave me the place in Graz… The hotel where I'd stored the Rambaldi box."

"He knew where you lived, he knew everything that the Covenant needed to abduct you. And, unlike your father, he didn't know that the training you were subjected to under Project Christmas – or Project Prodigy if that's what really happened – would keep you from being brainwashed by the Covenant."

I nodded. So it really was Sloane who had been responsible for my disappearance – the two years of my life that I had spent as another woman. When I came back, I challenged him, saying that I knew the responsibility for what happened to me rested on his shoulders, just as with SD-6… And then when he denied it I, stupidly, believed his words.

He lied. Of course he lied. He always lied.

"Director Dixon?" We both looked up to see my father had entered the room, just sticking his head in the door. "Is this a private meeting or may I come inside?"

"Jack. We need to have a conversation," Dixon said, his face steeled. My father came into the room. I saw that he had the black folder – the one from Wittenberg – with him, under his arm.

"Yes. I imagine Sydney told you about this?" he asked, showing the folder to Dixon. He nodded in reply.

"She told me that it was a CIA-sanctioned project to program her to find and destroy Irina Derevko. A project that you began when Sydney was born?" Dixon asked, still looking at Jack. I could see that he wasn't happy about what I had said about the files. Neither was I, but still…

"I have to go," I finally said, getting to my feet.

"Sydney, wait-" my father started, but I interrupted him, holding up a hand to stop him from saying anything more.

"Don't. Please, Dad, I just… I can't do this right now. I have to go home. Get some sleep." With that, I walked out of the office.

OOOOO

I went back to my apartment. I saw some of the other agents at the Rotunda, giving me questioning looks as I passed by them again and left the office. Dixon told me that I should to be back first thing the next morning – they wanted to run me through a debrief and make sure that I was all right after everything with my father and with Lauren in Palermo.

Once I was back home, I collapsed onto the couch. I was too exhausted to do anything but just sit there for a long moment, even when I heard someone knocking on the door. They'll go away, I thought. They'll figure I'm not here and leave, and then maybe I can get some sleep.

"Syd! It's me, I know you're in there, I just saw you in the parking lot." Weiss. I sighed, getting up and going back to the door. I opened it, seeing Weiss there. He rose his eyebrows at me in question. "What the hell is going on? I haven't even seen you in days, Dixon said you vanished again."

"Weiss, it's a long story," I replied with a sigh, leaning against the doorframe.

"Vaughn found you in Palermo. He killed Lauren?" he asked. I nodded.

"Yeah. Last time I talked to him, he was going back to the Rotunda. He had some things to answer for, after… What happened. I went to Wittenberg, there was something I needed to do."

"Come on, Syd, you're being so vague," Weiss said. "We're friends, right?"

"Of course," I stated.

"Then tell me what's going on." I sighed again, looking down at the floor to avoid his questioning gaze. Truth was, I wasn't even sure I accepted what I learned. That my father programmed me to be a spy – that he wanted me to kill my mother. That Sloane really was the one responsible for my abduction.

"Can we talk tomorrow?" I asked. Weiss looked at me for a long moment, not satisfied with my answer. But, eventually, he nodded.

"All right," he said. "Tomorrow."

"Thank you."

OOOOO

After almost three straight days of questions and lie detector tests, evaluations and medical checkups, they released from the Rotunda and – finally – allowed me to go home. The only problem was, home was the last place I wanted to go. 'Home' was still a place full of things that belonged to Lauren – full of those lies that I couldn't stand to be around any longer.

So, I called Weiss. Of course, he sounded concerned, after I disappeared from the hospital, threatening him and a couple of senior agents at gunpoint, and then left for Palermo. I wanted to explain everything to him, and have someone to talk to that wasn't going to question every word I said.

And, calling Sydney seemed out of the question at this point. I didn't even know whether or not she returned from Wittenberg yet.

Weiss and I met up at a small café not far from where he lived, close to the beach. It was quiet, and gave us the chance to talk about things. I wasn't worried about anyone overhearing our conversation, so I explained everything that happened from when I left the hospital up until calling him that evening.

"So… You killed Lauren?" he asked, obviously more concerned with that than with any of the lie detector or psych evaluation situations I described.

"She could have killed both of us," I replied. "The agency let it off as self-defense. I was defending myself and the safety of another agent." I shrugged a little.

"Yeah, but still, you shot your wife," Weiss stressed again. I shook my head.

"I shot a traitor who was pretending to be my wife," I corrected. Weiss nodded a little. "This whole thing… It's screwed up, and I'm prepared to deal with that, but I refuse to let it destroy me."

"You know what? That's actually a really good point of view," Weiss replied, nodding a little. I didn't reply. "So… Have you talked to Sydney?"

"No," replied. "Last I knew, she left for Wittenberg. I don't even know if she got back yet."

"I saw her at her place this afternoon. She seemed concerned about something. Upset I guess? Wouldn't tell me why, though," Weiss replied. I just nodded a little. "You haven't tried to call or anything?"

"It's complicated," I replied.

"Right. Complicated. Because?" he asked. I smiled a little in annoyance, shaking my head. "Come on, I just don't get it. She died, you got married, you left the agency, she came back, you found out that your wife was a traitor, she tortured you, and you shot her… What's left to figure out?"

"Can you just drop it?" Weiss's shoulders fell, and he shook his head, looking off into the rest of the café. "Look, I just…"

"No, it's cool. I shouldn't bug you," he corrected. I sighed, nodding in agreement.