Sydney is stunned when she learns that her mother was a KGB agent. The news is too much for her to bear, 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. By the time that Sloane realizes what is going on, the intruders have taken control of the building.
As Sydney enters SD-6, Jack catches up with her in an elevator. He 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 procedureÖwhich can mean only one thing -- someone has broken into SD-6...
Sydney and Jack sneak from the elevator, and make their way to an empty room in the basement. By splicing into the surveillance system, Jack and Sydney discover that the intruders have taken everyone hostage including Sloane.
Meanwhile, Will Tippin decides that the SD-6 story is too dangerous to pursue. Daniel Hecht and Eloise Kurtz have already been killed, and he fears the same fate for David McNeil's daughter if he continues.
At the newspaper office, Will receives another call from the mysterious voice. Will insists that he is no longer pursuing the SD-6 angle, but someone doesn't want him to give up. An unmarked envelope, containing another clue, is waiting on Will's chair. He refuses to open it, as he wants nothing to do with SD-6.
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 outÖWhat will it unlock?
After learning that Sydneyís mother killed his agent father, Vaughn receives orders to visit a CIA psychiatrist -- Barnett. He insists that he is fine, but Barnett asks about the Christmas gift for SydneyÖ Barnett wonders if his relationship with Sydney is "appropriate."
Vaughn confronts Haladki, the agent who informed Barnett about the giftÖ 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 SydneyÖ