Season 3
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Sydney is where we last left her, in a Hong Kong safe house. Vaughn tells her she's been gone for two years. Will survived the apartment fire, he says, but she died and her remains were identified. Vaughn's now a teacher, but the CIA sent him to take her back. Syd attacks Vaughn and escapes the safe house. She fights two CIA agents standing guard and Vaughn finally brings her down with a dart.
She wakes in the Stafford Naval Hospital. Dixon is there; he's now director of their division. Weiss calls Dixon away — he says Agent Scott Kingsley has the chip and is on a train to Avignon. He says the Covenant is moving to intercept and get the chip. A lead has placed a Covenant outpost outside Paris. Dixon returns and reveals that Jack has been in solitary for a year, courtesy of NSC Senior Director Robert Lindsey.
On train in Lyon, France, a gunman shoots and kills Kingsley. He finds the chip. It shows the schematics for an undetectable spy drone that, the CIA believes, could be used as a bio-weapon delivery system.
Sydney sees Marshall and Carrie, who is pregnant. In a meeting, Syd tells Dixon she was held captive in The Covenant's Paris base and heard Kingsley's name. Kingsley is just one of eight recent murders of CIA agents. Lindsey's adamant that Sydney go on this mission. Syd agrees on the condition that she gets to see her father. Lindsey agrees.
Syd tells a handcuffed Jack, who's been charged with resisting authority for contacting Irina (#6 on the CIA Most Wanted List), that she lied about The Covenant's Paris outpost in order to see him. He urges her to regain her CIA clearance and continue his research into her disappearance. He knew she was alive and has evidence. He also tells her that Vaughn isn't worthy of her grief.
In a Paris hangar, Weiss leads Syd and small team looking for the chip. They are attacked. Weiss is knocked unconscious and his throat about to be slit by the man on the train. Syd saves him. She admits she was lying and now if she goes back, her clearance will be pulled. Syd must identify this man. Weiss advises her to see Sloane, who now runs the World Health Org. in Zurich and is a consultant for the CIA.
She barges into Sloane's office. He was expecting her and identifies the man — Gordei Volkov — a Russian hitman. Blaming him for her predicament, she threatens to kill Soane. He says he's been redeemed, that the Rambaldi device delivered a message of peace. He then gave the CIA info to dismantle two dozen terrorist cells. Syd doesn't buy it.
Finding an old contact, Syd discovers Volkov has a meeting in Prague. She ambushes him, blows up his car. In the ensuing melee, Syd stabs him and retrieves the chip as he dies. She returns to Lindsey, threatening to destroy the chip unless he releases her father. He acquiesces.
Vaughn meets Syd. She's angry with him for looking for closure. She says she would have had faith and waited. But now she realizes it would have been an absolute waste if she had.
Jack returns to the CIA and takes Syd to a storage room. He shows her videotape of a Russian diplomat named Andrian Lazarey. On the monitor, a blonde Sydney stabs the man in the neck, killing him.
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