Sydney is brought to a torture room but the interrogation is halted and Russek becomes the target of SD-6 suspicions. He is tortured, and finally executed.
Sloane confides in Sydney about the intercepted communication from Switzerland, and that it was a message from Russek to K-Directorate. A confused Sydney asks Vaughn, who is equally perplexed.
With Christmas approaching, Vaughn gives Sydney an antique frame. This gesture arouses jealousy in Will, although he has just begun an affair with his assistant Jenny, which Sydney knows about.
For her next mission, Sydney is sent to Semba Island, just off the coast of Kenya. SD-6 is still trying to track down Ineni Hassan, and they believe that a forger on the island has created a new identity for the rogue arms dealer. On the island, Sydney discovers that Hassan has had plastic surgery, and now goes under the name Nebseni Saad.
Sydney hides this fact from SD-6, but Sloane already knows. He then instructs Jack to go to Cuba, where Hassan/Saad is now hiding. Sloane wants Hassan dead, though Vaughn proposes a counter-mission. Jack is asked to make a deal with Hassan: In exchange for Hassan's client list, Jack would then fake Hassan's death, which would stop SD-6 in their pursuit...but also allow Hassan to pass into the CIA's hands.
Meanwhile, Will studies the tape that was left in his car. With help from his audio engineer friend, Nevil, he discerns some muffled dialogue. The person who killed Eloise Kurtz said the name "SD-6."
Will researches the name, but finds only a single reference in a transcript from a lawsuit against David McNeil, an expert in computer encryption, who is now in jail for embezzlement. Will questions the lawyer, Robert Stoller, who says that McNeil only pleaded guilty after his wife killed herself. Will visits McNeil in jail, but the man seems genuinely scared at the name "SD-6." Refusing to talk, he demands that Will leave the lawyer alone.
From Vaughn, Sydney learns that her father made it appear that the intercepted communication from Switzerland was actually sent by Russek to K-Directorate. Vaughn then reveals that Jack is now being held captive by Hassan in Cuba.
Secretly, Sydney sets out to save her father. She is captured and brought before Hassan, just as Jack is explaining his unusual deal to the arms dealer. Hassan recognizes Sydney as an SD-6 agent, but is unaware of her connection to Jack.
Tempted by Jack's offer, Hassan needs him to prove that he is no longer loyal to SD-6. As a test, Jack must kill the captured SD-6 agent. A gun is placed in Jack's hand. He takes aim directly at his daughter.
Jack: I need you to tell me what's happening!
Steven: You didn't hear this from me. ... While Sydney and Russek were in Geneva, a transmission was recorded from her location and it was not one of ours.
Jack: You think it was Sydney?
Steven: This is not the first indication that she might be working for someone else.
Sloane: For the past few weeks, you've been under suspicion. We knew we had a mole and there were signs that indicated that it was you. And then when you were in Geneva, we picked up a third-party transmission and it seemed to confirm that you betrayed SD-6. And what I just learned is that it wasn't your transmission. It was Russek's.
Sydney: In the cell, when Russek was trying to get me to talk, I asked him questions about his interrogation. When he told me that they threatened to kill him, he was blinking at erratic intervals -- a classic indication that he was lying. So, I didn't talk only because I knew he wasn't in any real danger. Either Sloane still thinks I'm the mole and is using me somehow...
Vaughn: (embarrassed) I don't know. I was in this store, you know, um... this little antique place.
Sydney: (big smile) What were you doing in an antique store?
Vaughn: I don't know. (laughs nervously) Whatever. Um, look, if you don't like it just... don't tell me.
Sydney: Look, to you, my job might seem pointless and stupid but it's not. It's far from pointless and if you knew what I delt with every day, you might even thank me for doing my job so well!
Will: (confused) What the hell are you talking about?
Sydney: Nothing. I'm going to work. I'll see you guys.
Jack: Russek. It was a shock. ... What? Do you mean did I engineer it somehow? No, Sydney, of course not.
Sloane: . . . I didn't know how it would finally materialize: the darkness. I had nothing to base it on. It wasn't as if the C.I.A. had just betrayed me, that my wife had just been diagnosed with lymphoma. None of that had happened yet. So, whenever life takes an unfortunate turn, as it has this week, I just remind myself that I could see it coming all along.