“The Two”

Alias season 3, episode 1
Original air date: September 28, 2003

As Sydney wakes in Hong Kong and meets Vaughn in a safehouse there, he reveals a number of surprises about the occurrences of the past two years, including his new marriage and the fact that he's left the CIA. Sydney accuses him of lying and not really being Vaughn. She fights a number of agents in the hallways of the safehouse, trying to escape, until Vaughn knocks her out with a tranquilizer gun.

When she comes to again, she's in a military hospital, and Dixon comes to see her. Dixon explains a few more pieces of the puzzle to her, such as the fact that he's now the head of their division instead of Kendall. Wiess interrupts them to discuss something cryptic in the hallway with Dixon. An asset of theirs named Kingsley has received a "package" in France, but is in danger and can't be contacted. When Dixon returns to the room, he reveals that Jack is in solitary confinement in prison under the orders of the National Security Council. The asset on the train is killed, along with all other passengers, and the package he was carrying — a microchip concealed in a coin — has been taken.

Sydney tells Wiess she knows where she was held for the last two years. She mentions Kingsley's name, and Dixon adds her to a team that's raiding an outpost of a group called the Covenant, over the objections of Robert Lindsay, the CIA's National Security Council liaison. Kingsley's package was the schematics for a spy drone that can deliver biological weapons, which he had developed and was turning over to the CIA, and the plans are now in the hands of the Covenant. Unfortunately for everyone involved, though, Sydney was just bluffing — she had only read Dixon and Wiess' lips through the glass at the hospital, and so mentioned Kingsley's name to use as leverage to be able to see her dad.

The plan worked, though. Sydney's allowed to see her father, and he tells her that he was imprisoned for resisting authority. He contacted Irina Derevko for help in tracing Sydney's death, and when Robert Lindsay found out about their collaboration, he had Jack arrested. Jack says that Lindsay was trying to make an example out of him as being traitorous to his country. However, he also informs Sydney that he was hot on the trail of what had happened to her: he learned things that were very disturbing in the course of his investigation, including the fact that Sydney was alive, not burned to ashes in her apartment fire, as the CIA believed.

Sydney goes on the raid, but they find the building abandoned. Some of the Covenant's men attack, and most of the agents are killed. Sydney saves Wiess' life by startling the same Covenant henchman who killed Kingsley on the train as he's about to slit Wiess' throat. She reveals to Wiess that she was only using the Kingsley connection as leverage to see her father, but she now believes that she needs more leverage to get her father released from prison. She goes rogue and leaves Wiess to find more information on the Covenant.

To track down the henchman with the chip, Sydney turns to Arvin Sloane who is now running an international aid organization. He's prepared for her, and tells ehr that the man she's looking for is a Russian and a former hit man named Gorde Volkov. She questions the fact that Sloane just happened to have a file on Volkov laying on his desk, and he shrugs it off as simply knowing Sydney so well that he was waiting for her. She attacks him with a knife, and he tells her a story about how when he assembled the Rambaldi device, its message was a single word — peace — which turned Sloane's life around. He claims that he's changed his ways completely and is now trying to atone for his years of evil. Sydney doesn't buy it for a minute, but she's shaken by his calm.

She stands in an alley in Prague waiting for Volkov to come around, dressed in a sexy red dress. When his car comes along, he gets out, she blows it up — and all his men with it — and takes the chip from him. He comes after her with a knife, but as they're fighting, he ends up with his own knife in the stomach. Upon returning to CIA headquarters, Sydney's able to trade the chip for her father's freedom, just as she'd planned.

She confronts Vaughn about his marriage, saying that he lost faith in her and their relationship when he believed her to be dead. She claims that if the situation had been reversed, she would have waited for him, regardless of any DNA evidence presented to her. (I say "claims," because her fiance was dead less than a year before she had the hots for Vaughn.) She informs Vaughn he'll get no closure from her.

Jack also returns to the CIA, and when he does, he reveals to Sydney how he knew she was alive. He was on an operation, a year after her disappearance, tracking a Russian diplomat and spying on his personal office. He shows Sydney a tape of the man at his desk, when a woman comes into the office. The woman is Sydney, with long blond hair, and after talking with the diplomat for a few moments, she slits his throat from behind.