While Jack aims the gun at Sydney, under orders from Ineni Hassan, he blinks a message to her in Morse code. With precision timing, Sydney and Jack take down Hassan's thugs and capture the arms dealer. They whisk Hassan away, and Jack photographs a "deceased" Hassan. Sloane is duped into thinking that Hassan is dead. In reality, the one-time ally of SD-6 is in CIA custody.
After the mission to Cuba, Vaughn meets with Sydney, and tells her that he investigated the Cyrillic codes from her mother's books. The codes were orders written by the KGB and contain the names of CIA agents who were killed many years ago.
Sloane briefs Sydney and Dixon on their next SD-6 mission. One of Hassan's associates, Minos Sakkoulas, has taken his place in the criminal underground. Sakkoulas has a device, known as "the Package," and Sydney must travel to Greece to get data from Sakkoulas' computer. As a countermission, Vaughn gives Sydney a set of false files. She is to give these files to SD-6, while giving the real info to the CIA.
Vaughn and Sydney again discuss the Cyrillic codes, and both are convinced that Jack collaborated with the KGB. Sydney is reluctant to move forward with the information but Vaughn secretly records their conversation as evidence.
Sydney is unable to break into Sakkoulas' office so Dixon downloads the files. Later, Vaughn reveals to Sydney the secret recording. He also explains that one of the murdered CIA agents was his own father. Sydney is upset and seeks solace in Will Tippin's arms.
Hassan informs Vaughn that "the Package" is hidden in an abandoned missile silo on Crete. He also asks the CIA to bring his wife and son to the States for protection but Vaughn refuses.
Jack also tells Sloane about the missile silo. Sloane believes that Jack learned of this through his own contacts and sends Sydney to retrieve it. With Hassan apparently cooperating, Sydney breaks in and Vaughn guides her via satellite. At the point of entry, Hassan provides a false code to the silo's alarm system. This activates an anti-intruder device and the room begins to shower gasoline.
Hassan refuses to supply the correct code until he receives a written guarantee that his wife and son will get protection. Vaughn and Weiss agree and Sydney returns to LA with the device.
Sydney and Vaughn visit CIA Director Devlin with the evidence about Jack. But they are stunned when Jack, Devlin and other senior officers enters the room. Jack reveals that he never was a KGB agent, that it was Sydney's mother.
Sydney: Dad, can I ask you something? When you started with SD-6, you knew that they were a mercenary group and that they had no connection with the C.I.A. But I didn't. When I joined, I thought I was going to be saving the world and not making it more dangerous.
Jack: What's the question?
Sydney: Why didn't you say something? I mean, you could have told me what I was really doing - damage instead of good - but you kept quiet.
Jack: (sighs) Revealing the truth about what you were doing would have required revealing the truth about what I was doing.
Sydney: What happens when someone you care about is in trouble. What you said, that nothing else matters. It all just goes away. Last week when I learned what my father did for me, sacrificing Russek, it made me sick. But now, I know I would have done the exact same thing. You should have seen him.
Vaughn: Your father?
Sydney: Yeah, he was like ... he was like a pro. He was good. I mean, the way you talked about him once, what his reputation was, I could see it in action. He was ... impressive.
Vaughn: There's nothing routine about that list. There's something very specific about it. It's been a mystery within the agency for over two decades. Who murdered those C.I.A. officers? I'm sorry, but we have our answer now. It was your father. And I'm going to report him.
Hassan: Listen, I have a wife and a son. They are a target. Not just SD-6. I've made many enemies in the past. Now, you bring them to the United States, give them protection. You do that for me, and I'll tell you whatever you want to know. Everything.
Vaughn: Let me make one thing very clear, Mr. Hassan. The extent to which I am willing to service you is when I offer you a soda. There is no room for negotations. There are no perks coming your way. You have nothing to gain here!
Sydney: (from Hassan's weapons storage in Crete) Vaughn, what's going on? The room just went into lockdown!
(Back at the C.I.A.)
Vaughn: What the hell did you just do?!
Hassan: I gave you the wrong code. Your agent has activated an anti-intruder device.