Disclaimer: Alias does not belong to me, same goes for all the characters in this fic. They all belong to JJ Abrahms and ABC and Mutant Enemy and all of that. This is simply my way to deal with the dead time before the next season begins, so please don't sue.

A/N: This is my version of Season Four. Some of it is how I'd like things to go, some of it is experimentation, some is how I think it might actually turn out. Anything I get right/wrong is pure accident. Also, in addition to separating this into chapters, I've separated it into 'episodes', mostly as a way to help myself keep it all organized. The story as a whole, as well as the first episode, are titled Unraveling, and everything from there has it's own episode title. Hope that isn't too confusing! :-) I'll use OOOOO to signify change in location or time ot POV.

This is my first fanfic, so reviews would be greatly appreciated.

Unraveling
EPISODE 4.01

"Sydney." I looked up from the papers clutched in my already shaking hands, seeing my father. He followed me here from Los Angeles. Even though I hadn't told anyone my plan, he found me. "You were never supposed to have found this."

"Dad…" I looked down at the papers again, tears in my eyes. Documents so secret he'd locked them in a secure bank safe deposit box in another country. How I had come across all of this… It was practically impossible. A dying woman gave me the number, insisting that both of us were pawns in the same game. I came here, wanting to prove her wrong. I wanted to prove that she lied to me, as usual, and that I wasn't a pawn.

The classified CIA folder with the black-light paper was the last thing I expected to find. The documents I held were so classified that accessing the folder was almost impossible. The paper was all black, readable only with a UV lamp that I brought with me from op tech in Los Angeles.

As for the file… It was a project, initiated by my father, the day I was born.

Project Prodigy.

Three years ago, I learned that my father had programmed me to be a spy. He developed a program called Project Christmas. Training children as sleeper agents, so that when the time came, they could be recruited into the CIA and made into super-agents. Strong, intelligent, already trained to use weapons and think in ways most people would never understand. Observant.

These documents revealed something even worse.

"Listen, Sydney, whatever led you to this room-" I cut him off, standing and looking at him. Serious. Angry.

Betrayed.

"You should have told me about this!" I snapped. The preliminary documents in the folder didn't relate specifically to me, or to any of the programming used on me when I was a child.

The documents concerned my mother.

My father planned to use me to do to my mother what she had done to him. Everything I went through – believing my mother was dead, getting recruited into SD-6 and then finding out the truth and becoming a double agent, finding out she was alive and that she was KGB, trusting her only to have her betray me and escape and then try to regain my trust – was all a part of some plan. A setup.

He tried to use me to get to her. What was worse, it was in a project sanctioned by the CIA. Everything that happened would eventually drive me back to my mother. I would track her down, find her when no one else could, and bring her to some kind of justice.

Manipulated from minute one.

A million questions flooded into my mind, but I couldn't bring myself to ask them. Mostly, I didn't want to know the answers. The first thing I wanted to ask was if my father had arranged my abduction. The Covenant, capturing me, making me volunteer to lose two years of my life… Had that been a part of his project? Had he planned for my disappearance?

Everything I lost… Will, Francie… Vaughn.

"Sydney… You have to understand, I had no intention of ever activating the last phase of this project," my father tried again.

"Stay away from me," I spat through clenched teeth. He didn't try and stop me as I walked past him, and out of the bank vault. I didn't care what his excuses were – I didn't want anything to do with people that would use me.

He is no better than Sloane.

OOOOO

I didn't go back to LA right away. I needed time to think – somewhere where no one would bother me. I needed to try and figure out what had happened, what I had been through… Where everything stood now that I knew I could no longer trust my father, or anything he said.

Lauren Reed told me where the documents were. I tracked her to where the Covenant started a search for a new Rambaldi artifact, and we fought. She told me that I was a pawn – that we were both part of the same game. I ignored her, and she told me the number of the box just before she fell into the chasm. Vaughn shot her. He came after me, wanting to make sure I was all right.

That wasn't because of his wife – that was because of my aunt, Katya Derevko. My mother's sister. She came to us before, giving us helpful Intel. She even helped my father rescue Vaughn and I from a prison in North Korea, where – without her help – we faced execution. However, she was a traitor. I didn't know what her endgame was – just that she had stabbed Vaughn and then tried to kill me. I took the bullets out of her gun, knowing that she'd turned on me when she tried to put a bullet in my head from behind.

Then, there was my sister. I recently learned that my mother had an affair with Arvin Sloane – a man I considered to be my arch-nemesis. That affair gave them a child, my sister, Nadia Santos. I'd rescued her from a woman's determent camp in Russia, bringing her to a safe house. Sloane abducted her from there, using her to get a Rambaldi equation.

That equation apparently led to a Rambaldi artifact; something called the 'Sphere of Life'. I knew all along that Sloane had some more sinister endgame. When I came back from my missing two years – I knew what had happened though I still had no recollection of any of that time – Weiss told me that Sloane was a good guy. He received a pardon from the US government.

The government officials that granted the pardon revoked it just a few weeks ago, and Sloane became a rogue agent. My father faked his execution, as we needed his help to find my sister. Shortly after he had been reunited with his daughter, he and Nadia disappeared. She'd been found in Japan by our CIA tactical team, and taken to a safe house back in the US until we knew what to do with her.

The day I left for Wittenberg to look for the bank box Lauren directed me to, one of the agents at that safe house told me that Nadia had left. Presumably, she was somewhere with Sloane. Whether he abducted her or she left of her own free will was something none of us knew – I naturally suspected the former, but there was no way to be sure. We still didn't have any idea where Sloane went after Japan.

So, that was where things stood. The North American cell of the terrorist organization known as The Covenant – the ones that had abducted me over two years ago and tried to brainwash me to work for them – no longer operated. That cell, run by Sark and Lauren – who was a double agent inside the NSC for the Covenant, in addition to being Vaughn's wife – would flounder without its commanders. Sark hung, once again, in the precarious balance CIA custody. Lauren died, for all I knew, in Palermo. Of course, I hadn't checked, so I didn't know if she survived or not. I would find out eventually, I knew that.

As for the CIA, I couldn't go back until I was sure that I had been cleared of all suspicion. When Lauren realized that he CIA knew she was the Covenant mole, she disguised herself as me, breaking into the CIA operations facility at the Rotunda and attacking many of the agents there. And she shot Marshall, the op tech specialist and one of my friends. I had no idea if he was all right. Among the injured and dead were several other agents an analysis techs, and – of course – the internal investigation believed that I was at fault because of the way Lauren disguised herself.

Of course, that was days ago. I imagined that, by now, they would have interrogated Sark and found out that Lauren was, indeed, the woman that attacked the Rotunda. They wanted her taken into custody, but when she had tried to kill me, Vaughn shot her at least five times, and then she fell into the pit they'd been digging looking for the Sphere of Life.

After that, I told Vaughn that I was going to Wittenberg. I didn't give any specifics; just that I needed to look for something. I had to know if Lauren was telling the truth – if there was a document somewhere that proved what she had told me. About being a pawn in someone else's sinister game. He'd gone back to the Rotunda, classified as a rogue operative himself after he had beat information out of Sark and then gone to kill Lauren himself. Then Katya had appeared and stabbed him.

So, there was a lot to be sorted out.

Just once, I found myself wishing, I wished that I could have a normal day. Some day when I didn't have to worry about who I could trust, who told me the truth and who lied. And, since I had come back from my missing time, a day when I didn't have to see that pained look on Vaughn's face when he thought of everything that we had before I had disappeared. That look that had gotten so much more complicated once he found out who Lauren really was – whom she really worked for.

I wanted to believe that everything could go back to the way it was before. That we could just pretend that the last several years hadn't happened. I'd never disappeared, he never got married… But the intensity of everything that happened, the things we'd both been through… I knew that made it impossible.

I disappeared for two years. He thought I died in a fire at my apartment. I had later been told that I had been present at my own funeral, watching him spread my ashes at sea. He moved on with his life, getting married and leaving the CIA to become a French teacher. When I came back, he started working with the CIA again.

Over the last year, we'd gone through a lot. Lauren tried to be nice to me, finally giving up when she realized that her husband still felt something for me. That I still loved him just as much as I did before I disappeared. Vaughn tried to separate from her, but her father died suddenly and he'd gone back to try and comfort her after his 'suicide'.

It wasn't long after that that we learned that she worked for the Covenant. She betrayed him – their whole marriage was nothing but a lie. She tried to coax him back into the CIA, so that the Covenant could literally sabotage our operations. Not only that, but her mother worked for them as well, and had been the one responsible for the death of her father.

My father had told him to kill Lauren. He'd tried to do it. Stalked her, tried to murder her. Katya stopped him, but he ended up shooting her anyway when he came to rescue me at the dig site.

I couldn't begin to imagine the effect that all of that was going to have on him. And, as much as I wanted to be there for him, I wasn't even sure that he would want me to be there. After everything that happened… I wasn't sure he was ever going to be the same person.

Which scared me.

OOOOO

After going to Palermo to track Lauren and Katya Derevko, Sydney went to Wittenberg in order to look for something she thought might be important. Which left me to go back to the Rotunda alone and try to explain why I threatened two senior CIA officers at gunpoint, escaped custody after attempting to murder a suspect ordered to be taken into custody, and disappeared into another country.

Which, needless to say, wouldn't be easy.

The minute I walked into the Rotunda, two of the security team members came up to me and escorted me into a side office used for officer interrogations. One of the directors of the CIA, a man named Mark Newman who came to the Los Angeles base for a meeting with Dixon, waited in the room. I sat down, and he dismissed the two security personnel.

"Agent Vaughn," he addressed me, leaning forward and placing his elbows on the small desk that separated us. "I'm sure you understand why you've been brought in."

"Yes," I answered shortly. I knew I had a lot of explaining to do, but I didn't want to start making excuses and make myself look guilty or like my judgment wasn't trustworthy. Which, in all honesty, it probably wasn't. Finding out that my wife was a double agent for the Covenant and having her torture and attempt to kill me probably affected me more than I wanted to admit, even to myself.

"After the discovery that your wife, Agent Lauren Reed of the NSC, worked for the terrorist organization known as the Covenant, you were instructed to continue as usual, not to let her know that the CIA was aware of her double agent status," Newman began. "When she discovered the truth, she and Julian Sark abducted you, trying to get information on someone referred to as "The Passenger". Information, which, when subjected to the Inferno Protocol, you gave to the Covenant.

"Once released from the hospital, you began forming a rogue operation to carry out the assassination of Lauren Reed. I suppose the most obvious question would be why you ever thought such drastic action was necessary?" he asked, eyebrows risen in question. I took a deep breath, and began explaining.

"After I realized that Lauren was not only sabotaging our missions, but that she was actively involved in a plot to kill me and other members of this agency, I didn't think just taking her into custody seemed appropriate," I replied.

"And the weapons? The resources you had for this rogue op? Where did all of that come from?" Newman questioned.

"A contact of mine. A freelancer," I lied.

Really, the facility I'd used – the weapons, the 'disposal facility' – came from Jack Bristow. Several months ago, we worked with Sloane and another man named Thomas Brill to break Sydney out of NSC custody when the head of the NSC, Robert Lindsay, thought she murdered a Russian diplomat named Andrian Lazarey. I'd seen the facility then, and Jack gave me the key and insisted I kill Lauren myself rather than obsess over her betrayal for the rest of my life.

"I assume you're not going to give me a name?" Newman questioned.

"If I knew a name, I wouldn't give it to you," I answered. He smiled a little, probably already trying to figure out one of the infinite ways he could make me talk. "I also think it's important to mention that I never intended to go through with her assassination."

"And why is that?" Newman asked.

I interrogated Sark. Beaten him would be a more accurate term. Broke his nose, dislocated a shoulder, things like that. Eventually, he didn't have a choice – he had to tell me where Lauren was. When he did, I went there. I followed her. Knocked her unconscious, threw her in the trunk of the car and took her to a warehouse in the middle of nowhere.

She tried to plead with me. To tell me that she hoped the Covenant wouldn't contact her after asking her to marry me to get secrets about the CIA's operations. I almost bought into it the first time, when she and Sark captured and tortured me.

This time, I knew she lied.

"I am going to erase you," I told her. I hung her from a pulley on the ceiling, her feet a few inches off the floor and arms stretched above her head. "I'm going to remove any evidence that you ever existed. You used me," I hissed, "you used my grief, my work, who I am. You took that from me. I'm taking it back."

She protested. Said she did love me, but that when Sydney came back I didn't need her anymore and she started working for the Covenant again because she felt 'useless'. I told her she was lying and never to say Sydney's name in front of me again.

Then I told her that I hated her. I hated her, but I loved Sydney more, and I wasn't going to antagonize her just to get revenge on the woman that betrayed me. So, I wouldn't kill Lauren.

"I know better," I finally answered.

"I'm sure," Newman replied, obviously not believing me. "Let's change the subject. A woman named Katya Derevko, sister of the infamous Irina Derevko held for several months at this very facility several years ago, attacked you. She stabbed you before you could do anything to Lauren Reed?"

"That's correct," I said with a nod. Just before I began torturing Lauren, Katya came up behind me and stuck a knife in my back. I collapsed. Luckily, I thought to hit the call button on my cell phone before I lost consciousness, so that the CIA would be able to track me. I woke up at the hospital.

"You were taken to Stafford Naval Hospital, where you seized a weapon from Agent Weiss and used him as a hostage to escape custody," Newman continued.

"The only reason I threatened other agents was because I knew Agent Bristow didn't have any knowledge of Katya's betrayal," I explained. "I had to make sure that she wasn't in any danger in Palermo when she went after Lauren."

"And the reason you had to go yourself has nothing to do with the fact that you and Sydney Bristow were once… Involved?" Newman questioned. I clenched my jaw, refusing to say anything for a long moment.

"I went because I was concerned about the safety of a fellow agent," I finally replied, keeping my eyes locked on Newman's. "I don't see what relevance any personal reasons of mine have to this discussion."

"Well, Agent Vaughn, because of your recent rogue operation and attempt to assassinate Lauren Reed, despite being ordered otherwise, I think your personal motives have every relevance," Newman replied matter-of-factly.

For a long moment, neither of us said anything. I kept my gaze locked where it was, and he finally looked away, shaking his head a little.

"In Palermo," he started again, obviously deciding to move on now, "you arrived after Agent Bristow disarmed Katya Derevko?"

"I saw her on the hill," I answered.

Once I was out of the naval hospital, I got to Palermo as fast as I could, hearing from Weiss that Sydney went there looking for Lauren. The location code that I got from her right before I abducted her led there.

When I arrived, I saw Katya, unconscious with a tranquilizer dart still in her shoulder, lying on the side of the hill. My plan was to take her into custody, bring her into the CIA and find out why she betrayed us. But, I heard sounds of a fight at the dig site below me, and saw Lauren and Sydney there.

I had a gun. I challenged Lauren just as she got Sydney in a headlock. She challenged me the same way Sark had just weeks before – if you love her, you'll put your gun down. Knowing that, if I didn't, Lauren would put a bullet in Sydney's head, I lowered my weapon. Then, when the opportunity presented itself, I shot her.

I think I shot her five times before she told Sydney a number – 1062 – and then fell into the pit that the Covenant unearthed, looking for a Rambaldi artifact. I explained all of this to Newman, insisting that I shot Lauren in self-defense, and that Sydney would back up my story when she came back from Wittenberg.

"And why did Agent Bristow go to Wittenberg, rather than return to Los Angeles with you?" Newman asked.

"I don't know," I answered truthfully. "She thought something important was there – that was what the number referred to, but she wouldn't say what. I don't think she knew." Newman nodded a little.

"All right. That's all for now. You're to report to medical services for a review after your injury and your exposure to the Inferno Protocol. After that, we have some tests we have to run. Standard procedure – you understand."

"Yeah."

"Very well. I'll see you in a little while, then, Agent Vaughn."