Season 2: Episode 3 - "Cipher"
 

Sydney learns the T-Wave Camera she had stolen was a prototype, and that the Asiatic Space Agency and their client Sark will launch the real camera, which can see 100 meters through solid matter, into space in 72 hours from a site in Sri Lanka. Her mission is to wire it so SD-6 can tap into the image.

At the CIA, Kendall wants Syd to talk to Irina because Sark has assumed control of her organization, so she must know what he's looking for. Meanwhile, Jack tells the CIA psychiatrist that he wants to keep Sydney away from Irina. She notes that Jack refers to his ex-wife as Laura.

Irina tells Sydney that Sark is after a Rambaldi-designed music box. Encoded in the tune is a numerical equation for 0-Point Energy. Sydney rebuffs Irina's attempts to talk about her childhood. Later, Jack warns Syd about Irina, but says he trusts her judgement.

Marshall gives Sydney a hydraulic luge disguised as a suitcase. A grieving Sloane gives her something more personal: Emily's seed box. As part of her counter-mission, Vaughn gives her a circuitboard to attach to the camera and suggests bringing in Will, who's been stying with Syd and Francie, because he may remember the code Sark was working on that activates the music box. When they do meet, Will is surprised at Vaughn's youth and is jealous at how much he knows about their lives.

In Sri Lanka, Sydney disguised in a red wig as a European business woman, appears at the launch facility as Dixon breaks down the surveillance. She then dons a worker's jumpsuit and luges through the exhaust ports to the launch deck. A suspicious Sark speeds the launch. Syd barely completes wiring the circuitboard and luges out at 125 mph. The camera locates the music box in the center of a Siberian ice cavern.

Under hypnosis, Will remembers the names on Sark's computer — Dosteyevsky, Nabakov, Tolstoy, Checkov. Vaughn notices Sydney's feelings for Will. Later, Irina decodes the names and warns Sydney about Sark's ruthlessness, saying she wants the chance to explain herself.

Sloane receives a ghostly call from the Baranka B&B in Sonoma, CA — where he an Emily were supposed to go before she died.

Back home, Sydney tells Will that she's glad she doesn't have to lie to him anymore and then leaves to eulogize Emily Sloane. At the CIA headquarters, Irina comes in from the cold and surrenders. Jack confronts Irina, who says they had their good moments together. He threatens to kill her if Sydney is harmed. She asks cryptically, "You haven't told her what you did to her after I disappeared, have you?"

In Siberia, Sydney receives the code from Vaughn and plays the music box. She records the tune and acts to disable the artifact. The SD-6 team is ambushed by Sark's men, however, and Sydney falls under the ice.