Clutching a stolen satchel, Sydney is dodging bullets and racing from French guards at the Machlet Corporation. Taking the nearest elevator, she punches the ceiling out and pulls herself out the top. Climbing the cables, she escapes onto the street to a waiting limo...
Back home, Sydney briefs Vaughn about her mission and the overall organization of SD-6. In her new role as a double agent for the CIA, Sydney is intent upon destroying SD-6 within a matter of weeks. But CIA Agent Vaughn illustrates for her that SD-6 is no small matter, it encompasses over 200 groups and contacts - and not just the LA bureau where she works. A humiliated Sydney accepts it will take a very long time to shut them down.
Later that day, her journalist friend, Will, confronts her about her recent disappearance...
...and asks what her fiancé Danny could have been involved with that got him killed. Sydney tells Will that she has been disoriented since Danny's death and to please leave it at that.
But Will's curiosity is piqued, and later, he learns and tells her that Danny had a booked flight from LA to Singapore the night he was killed...to which, Sydney must hide her shock.
Her first day back at SD-6, Sydney receives instructions from Sloane to travel to Moscow, and to intercept a sale of stolen files pertaining to Soviet-American nuclear arsenals. Afterwards, Sloane leads Sydney to his office, revealing her father Jack, who is waiting for her. In private, Sydney only wants to ask him one thing...whether SD-6's plan to kill Danny had been shared with him first. Later, Jack admits he was the one who bought the plane ticket so he could send Danny to Singapore, to hide from the SD-6 assassins. We learn that Jack had visited Danny's home that fateful night, only to find he was too late.
In Moscow, Sydney impersonates a hotel maid to gain access to the hotel room of the CRC’s representative holding the payoff money -- while Dixon meets the document sellers at a Moscow club. After a violent confrontation with the bodyguards, Sydney discovers the payoff money is false paper... Incognito in party attire, Sydney races to the club, and makes a fast switch with the two computer disks containing the stolen files - with two plastic cocktail coasters. Dixon and Sydney knock the agents out, and escape with the disks. At LAX, Vaughn makes a ”brush pass“ with Sydney, duplicating the stolen floppies for CIA, and returning them so she can present them to SD-6.
The information Sloane later retrieves from the disks, informs that a nuclear device from the Cold War period is still buried somewhere in the US.
Sydney's mission leads her to a Virginia cemetery, where she finds a tombstone with the contact's name, Ivanov, on it.
Digging up the grave, she finds the seventh nuclear device, rigged to the coffin lid. She calls a panicked Marshall who guides her through the process of disarming it with only a two minute warning.
Angry, Vaughn informs Sydney that SD-6 has sold the device to Ineni Hassan in Cairo, a known arms dealer. Since Sydney knows Hassan, she volunteers to make the trip and get the bomb back; making sure that SD-6 doesn't know that she's going there. Back at the CIA, Davenport tells Vaughn that he's being pulled off of the Bristow case because Devlin, the boss, wants a more senior officer assigned.
Meanwhile, Sydney and a male CIA operative go to Cairo. When Sydney finds the bomb, she quickly dismantles it and grabs its bright green core... only to find a gun is pointed at her head and cocked - and it's Hassan...