“Full Disclosure”

Alias season 3, episode 11
Original air date: January 11, 2004

After the cube that Sydney retrieved in Graz (with the vial of Rambaldi tissue inside it) is taken from the CIA by the Department of Special Research, Sydney asks Jack what they will do to figure out where she's been. The box was the latest clue that was getting her closer to finding it out, and now it's gone. It turns out that she doesn't have to wait long to learn the answers: she's hit with a tranquilizer dart in her apartment, and when she awakens, she's on a plane with former CIA Director Kendall. Seems he's now with the Department of Special Research, and he has all the answers about where she's been and what's happened to her.

He tells Sydney that he learned all of this from her, when she escaped from the Covenant in Rome about 9 months prior. But let's go through it chronologically. After the fight with Allison in their apartment, Sydney was taken by the Covenant. Another body was dumped in her place, and her DNA was injected into the teeth of that body, so that when the CIA tried to identify it — knowing that it would be burnt beyond recognition when the CIA found it — they would check the teeth and presume it to be Sydney. Sydney awakens in the back of a van on a beach. Dr. Oleg Matrijik, a Covenant doctor, injects her with a neurotoxin to paralyze her, while she watches her ashes being scattered by Vaughn at her funeral. Matrijik is the same doctor that Sydney killed at the beginning of this season, the one who said that Julia was his favorite and she had promised she'd kill him.

Matrijik then took Sydney to a Covenant facility near St. Petersburg to try and brainwash her into being Julia Thorne, concocting an entire life story for her and subjecting her to torture, food and sensory deprivation, and other methods to break her down. Julia was supposedly a trained assassin, a mercenary that the Covenant could use. When he was convinced that Sydney/Julia was well-enough prepared, he showed her to his bosses at the Covenant for them to test her. They ask her to kill an "unimportant man" right in front of them, and she does so without hesitation.

Sydney stops Kendall to ask about her brainwashing. He tells her that as part of the conditioning that Jack performed on her as a child, through Project Christmas, she couldn't be brainwashed by anyone else. He says that she was only pretending to have been brainwashed to earn the Covenant's trust, because she knew that was her only hope. As soon as the Covenant began using her as an assassin, she contacted Kendall and met him at a safehouse near Rome.

Kendall tells her that she has to stay undercover and let everyone think that she's dead, but she refuses. She says that she needs to see Vaughn and her father. Kendall won't allow it, because he knows that the Covenant will be tipped off to her double-cross and that both Jack and Vaughn will be in greater danger. Sydney defies him and tracks Vaughn down, but with dismal results: she sees him on a date with Lauren and, defeated, calls Kendall to say that she'll do whatever he says.

The Covenant sends her to kill Lazarey, so that they can get their hands on his money through Sark. However, Sydney goes to Lazarey beforehand and explains that unless he joins her and stages his death, he will be killed by the Covenant. Not being stupid, Lazarey agrees and works with Sydney to find the next Rambaldi artifact: the cube. Lazarey's been a Rambaldi scholar for 30 years, and so he's collected the 12 keys to the vault in Africa where the cube has lain for hundreds of years. Getting the cube, his hand is caught in one of the booby-traps, so Sydney has to chop it off.

But at that point, cube in hand, Sydney decides to go rogue. Instead of sending the cube to Kendall as she's supposed to, she sends him a video, saying that she wants to forget everything that's happened. She's going to have her memory erased, and she begs Kendall never to tell her what she's been through.

As it turns out, the Covenant wanted the cube and Sydney because they believe the Rambaldi prophecy that Sydney will be "the one to bring forth [his] greatest works ... unto utter desolation." Except they understand it a little differently than Sydney; they believe that with her DNA and Rambaldi's, they can produce a baby that will bring about destruction. Which explains the scars on Sydney's stomach. They've taken her eggs. And the reason that Kendall is sharing all of this with her, even though she has said she never wanted to know, is that the Covenant has manipulated her into revealing the cube to them, after she thought she'd safely hidden it from everyone in Graz.

Sydney pieces together that she got a key from Sloane, which led her to the apartment in Rome, where she found coordinates to dig up Lazarey's hand in the desert (which the Covenant had taken from the vault in Africa). She then tracked down Lazarey, who told her to go to Graz, where she found the cube. And now the Covenant has ambushed the Department of Special Research convoy that was transporting the cube, which means that they have Sydney's eggs and Rambaldi's tissue.

Kendall helps Sydney, Vaughn, Dixon and Weiss set up a raid on the Covenant facility where they're creating the test tube baby. Sark is overseeing the procedure, but he flees when the raiders show up. After killing Sark's men, Sydney torches the place, despite Kendall's orders to bring everything back for analysis. Weiss and Vaughn find Lazarey, and they transport him back to a hospital. He asks Sydney if she knows about "the passenger." She has no idea what he's talking about, but promises that they'll talk at the hospital. Unfortunately, Sark has called one of his minions and told her to get rid of Lazarey at the hospital. Lazarey's shot by a sniper, who turns out to be Lauren, although she's not found and no one in the CIA knows that it was she.