The Box, Part 1
The news that her mother was KGB is too much and she tells Vaughn that she is going to resign from SD-6. At the same time, a group of heavily-armed intruders sneak into SD-6 and take control of the building.
As Sydney enters SD-6, Jack warns her that the Alliance, the men Sloane works for, will kill her if she tries to quit. Their elevator comes to an abrupt halt, and Jack realizes that Sloane has triggered the emergency lockdown procedure.
They sneak from the elevator and make their way to the basement. By splicing into the surveillance system, Jack and Sydney discover that the intruders have taken everyone hostage.
Meanwhile, Will Tippin decides to quit the SD-6 story, but at the office an unmarked envelope containing another clue is on his chair.
The leader of the intruders is McKenas Cole, a former SD-6 agent who is now working for an unknown group. Cole tortures Sloane for the access code to the SD-6 vault. However, because of the security measures that have been activated, opening the vault will trigger an explosion.
Jack tells Sydney that the entire SD-6 building will be destroyed. In Marshall's workshop is a scrambling device that can be used on the vault door, so that even if Cole gets the code, the vault will not open. Sydney must retrieve the device without being discovered.
Meanwhile, Will goes to a restaurant to meet a contact for a story. To his surprise, it is Kelly McNeil who shows up. Someone has clearly arranged this meeting, and Will refuses to talk.
Kelly follows Will to his office and pleads with him to continue investigating SD-6. He is persuaded and finally opens the envelope that was left on his chair. A mysterious key falls out.
After learning that Sydney's mother killed his agent father, Vaughn receives orders to visit Barnett, a CIA psychiatrist. He insists that he is fine, but Barnett asks about the Christmas gift for Sydney. Barnett wonders if his relationship with Sydney is "appropriate." Vaughn confronts Haladki, the agent who informed Barnett about the gift. There is clearly bad blood between these two men.
Meanwhile at SD-6, Sydney retrieves the scrambling device and applies it to the vault door, moments before Cole arrives. Before Sydney can escape, Cole and his men hear her in the airshaft. They begin blasting away at the ceiling, the bullets narrowly missing Sydney.
Jack: I know how this feels.
Sydney: Not exactly. You've had a lot longer to make sense of this than I have.
Jack: There was a time when this was news to me, too. Your mother was sent to the United States to steal secrets from a ranking officer of the C.I.A. How she and I happened to meet, how she supposedly fell in love, I thought it was all true. But it was just a set-up.
Sydney: (voice over) There's something that happens when you discover the truth about someone. I know a little about this. The truth changes everything.
Sydney: (talking to Vaughn) There's this woman, her personality like a collage I've put together from the photographs, the few memories I have, scraps of stories I've heard, the clothes of hers I've got... her books. And none of it's real. She wasn't that woman at all. She was... she was a horrible person... who killed your father.
Sydney: Look where we are. I mean, this isn't real. This isn't what we should be doing. I want out.
Vaughn:You want to enter the protection program.
Sydney: No. I'm not going into hiding.
Vaughn: If you don't, Sloane will kill you.
Sydney: I don't think he will.
Sydney: How could K-Directorate overpower fifty trained agents?
Jack: If K-Directorate attacks SD-6, they know SD-6 will return the favor. This team that's invaded SD-6, isn't working with any organization we know. My guess is they're working for a group, clearly unpredictable and dangerous.
Jack: Sloane must have activated the emergency failsafe. There are five hundred pounds of C-4 strategically placed within the substructure of this building. Opening the vault will trigger that C-4. All underground levels will collapse, burying any evidence that the Los Angeles cell of SD-6 ever existed.
Cole: You're going to give me the combination to the SD-6 vault and if you don't, I'm going to open this box. And Arvin, trust me when I tell you, you do not want me to open this box.