Title: Skeletons in the closet

Summary: Sydney faces her past at SD-6.

Disclaimer: I don't own anything Alias related, only the characters you don't know.

Spoiler: 3:17 'The frame' and before, AU after that.

Rating: PG-13

AS Dixon drove up next to Sydney's car he found her sitting on the curb, her hair and clothes soaking from exposure to the rain. She sat sobbing into her hands as he approached her. "C'mon Syd, I'll take you home. You're obviously not in..."

"I'm not mad Dixon. I saw him. When he saw I was looking he ran. I chased him right onto the main road. Check the CCTV in the area. It will show me running after Danny." She choked through tears. "He's alive, and he runs the Covenant."

Several hours later Sydney sat in Marshall's office with a cold cup of coffee in her hands and tears staining her face. Marshall sat showing her pictures of little Mitchell trying to take her mind off things while Dixon had an IT specialist check the CCTV from the area Sydney had chased Danny in.

When the door opened her father stood there with a grim look on his face. "We've made a positive ID on the man you chased. He is Daniel Hecht. Dixon wants us all in the briefing room." Sydney nodded and he left. He couldn't console his daughter. After all the betrayal she had survived and all the lies he doubted she could easily get over Danny being alive and he hoped, for his daughter's sake, that Danny wasn't the Covenant leader.

When Sydney slumped down into her chair she saw Elliot and Zac sitting in Lauren and Vaughn's usual seats and a fresh wave of tears threatened to wash over her. Dixon began. "Now, everyone in this room, except Weiss, knew Daniel Hecht. He was Sydney's fiancé and a sleeper agent named Shepard was told to kill him. His body was clearly identified and he was buried. Tonight we have eye witness and CCTV to prove that Daniel Hecht is alive..."

"When I was being tortured by the covenant he was there. He'd try to get me to give up and become Julia Thorne. He said we would be happy again. After the drug therapy I received I remembered his visits, but I've seen him many times before since he died. I thought I was just imagining him. He told me he was the Covenant."

Zac's glare burnt into Elliot as she tried to conceal her guilt. "Tell them." Everyone's eyes snapped to the two agents as Elliot scowled.

"They don't have clearance." Elliot snapped. She didn't want to face Sydney finding out that she had kept something else away from her. Dixon was about to object when Elliot shook her head and began her explanation.

"Whilst working at SD-6 our CIA handler told Zac and I that there was a man connected to one of the agents that was vital to project black hole. He was Daniel Hecht. The last in the Rhambaldi blood line." Sydney allowed her words to sink in and knew the full meaning of them.

"He was with me to create the second coming. When SD-6 wanted him dead he couldn't just seduce me, so he stole my eggs and got me to work for him...and they say chivalry is dead." She muttered bitterly.

"The reason Danny never liked me was because I confronted him with what I knew. He knew it was a matter of time before the CIA found out about Sydney's connection to Rhambaldi. He had himself cloned using the prototype of project Helix. When Shepard came he killed the clone and Danny went into hiding."

"Now he controls the Covenant and all its resources." Dixon continued his brief. "If Daniel Hecht wants to bring the second coming then he'll want Sydney. I think we should put Sydney into witness protection straight away."

"I agree." Jack added. "It's not safe for her out in the open."

"No. Vaughn's still..."

"Vaughn is not your priority right now. We have a lead on his location. Elliot and Jack will be leaving for the rescue mission in two hours." Sydney went to rise but three armed CIA agents stood behind her. "I'm placing you under CIA custody for now. It's where you'll be safe."

"From Danny."

"From your pride."

She was escorted to the cell that had once housed her mother and Sark. She knew that before the Covenant had got her she would have never belonged there, but since she'd been Julia Thorne and learnt of what she'd done for the Covenant she felt just as putrid and guilty. Maybe she was no better than her mother. Maybe it was in her genes to be like Irina Derevko. A ruthless and feared assassin who would go to any length to get what she wanted.

When her father came to see her she said as much. He looked away from her eyes and shook hid head. "You are ten times the woman she is, never forget that. You are loved..."

"Danny loved me, he betrayed me. Elliot loved me, she betrayed me. Will loved me, he might as well be dead now, he isn't Will anymore. Noah loved me and...I killed him. Vaughn loved me and look at all the pain I've put him through. Anyone who gets close to me ends up hurt or betraying me..."

"I'm doing okay." Jack replied. His cold gaze settled on his daughter.

"Dad, you've only been close to me since you lost me and you have betrayed me since I was five years old." She said bitterly. He nodded in cold acceptance and left to do his mission with Elliot.

On the plane they sat in silence and Jack looked over the mission brief once more. "I need to know I can rely on you." He said suddenly and caught Elliot by surprise.

"Just because Vaughn loves Sydney doesn't mean my jealousy will get the better of this mission. Loosing Vaughn after everything that's happened would kill Sydney, so I'm bringing Vaughn back tonight, even if I have to risk my life to get him to her."

"When Sydney first introduced us at her birthday party I knew you'd protect her and I knew you truly did love her. I know you would have been better for her than Danny." Jack explained.

"Yeah, but then you knew what he really wanted. She still has no idea that when she introduced me to you that she was introducing a CIA agent to her handler." Elliot replied. "If she found out she'd hate us both."

"Then she can't find out."

A/N: It may seem a little far-fetched bringing Danny in but I promise I will make it work. Thankyou to everyone who has reviewed my work.