Alias season 2, episode 1
Original air date: September 29, 2002

Sydney's ordered to see a CIA shrink after returning from Taipei. (Shrink scenes allow for flashback retelling of the end of last season and the beginning of this one; JJ Abrams wasn't kidding when he said this season would be easier to follow!)

After Khasinau's men captured Sydney, she met her mother face-to-face for the first time in 20 years. Her mother asks who sent her, and Sydney refuses to answer, retorting, "Or what? I'm grounded?" At which point, her mother shoots her in the right shoulder and promises to ask her again. When her mom leaves the room, Sydney destroys the chair to which she's tied, then uses a fire extinguisher as a propulsion cannon through the door to get out. She fights some guards, etc., etc. (with a bullet in her shoulder!), and escapes.

She's supposed to rendezvous with her dad and Will, but she says she can't leave Vaughn behind. She steals a hazmat suit and goes into the warehouse to look for him, but only finds his jacket. She has to abandon him for lost and catch her plane. On the plane, Francie calls to say that Will's story's hit the paper and he's being splashed all over the news as a missing journalist. Furthermore, Dixon has reported Sydney's slip-up in Aconcagua to Sloane, so her cover looks to be blown. Jack realizes that they'll all be in danger as soon as they land, so he agrees to take full responsibility: he goes to Sloane and says that he gave Sydney the codename "Freelancer" during her Aconcagua trip, because he didn't trust Sloane. He also tells Sloane that Will doesn't know anything and that he'll make sure Will never writes another article. To discredit Will, Jack shoots him up with heroin, dumps him in a drug house in South Central L.A., and has him arrested in a police bust there. Will then speaks to reporters outside the police station and claims that everything he's written in his "three-year battle with heroin" has been fictitious.

Meanwhile, though, Sydney's gotten another mission from SD-6 - to plant a bug in one of Khasinau's operative's houses in France. She does so, at the same time planting a time-delay feed to the CIA, so that the CIA will be able to control what of the wiretaps SD-6 can hear. On her way out of the house, though, she recognizes one of the party guests as one of the hazmat clean-up crew at the warehouse in Taipei. She follows him to the basement where Khasinau is about to perform surgical experiments on Vaughn. Khasinau gets distracted by the noise Syd makes, and leaves the room, giving her enough time to stab Vaughn in the heart with adrenaline and get the two of them out of there.

Back in L.A., the CIA learns from the France wiretap that there's an operative's manual called "the Bible," which will allow Derevko (Sydney's mom) and Khasinau to rebuild their organization. Sydney, Weiss, and Vaughn arrange to intercept the Bible transfer in Barcelona, and because of the CIA interception of the wiretap, SD-6 isn't even aware of the Bible's existence. The interception goes awry when Sydney's mom turns up as a sniper on the roof, shooting Weiss and wreaking havoc on the whole operation. Sydney follows Khasinau, who's escaping with the Bible in a suitcase. She's got him on his knees at gunpoint when her mother comes in behind her, holding her at gunpoint. Sydney drops her weapon, and her mother shoots Khasinau in the chest, forces Sydney to her knees, takes the suitcase, and says, "Truth takes time," then disappears.

Will's recovering from his heroin nightmare and trying to figure out what he's going to do next. Francie's opening her restaurant, and Sydney's getting ready to eulogize Emily Sloane. At the funeral, Jack receives a call from Devlin: Irina Derevko just walked into CIA headquarters and turned herself in, saying she wants to help.