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 only as "the Package," and Sydney must travel to Greece to get information from Sakkoulas’ computer. As a countermission, Vaughn gives Sydney a set of false files. She is to give these files to SD-6, while retrieving 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.
In the Greek nightclub where Sakkoulas has his headquarters, Sydney’s plans are thwarted, and she is unable to break into Sakkoulas’ office... Instead, Dixon downloads the files, giving SD-6 the information they want.
Vaughn reveals to Sydney the secret recording of their previous conversation. He also explains that one of the murdered CIA agents was his own father. Sydney is understandably confused and upset, and she seeks solace in the warm embrace of Will Tippin.
Begrudgingly, Hassan informs Vaughn that "the Package" is hidden in an abandoned missile silo on the island of Crete. He also asks the CIA to bring his wife and son to the States for protection...but Vaughn refuses.
To justify Sydney’s trip to Crete, Jack also tells Sloane about the missile silo. Sloane believes that Jack learned of this through his own contacts, and Sydney is sent to retrieve "the Package" for SD-6...though she secretly plans to give it to the CIA.
On the island of Crete, Sydney breaks into the missile silo, with Vaughn observing via satellite. With Hassan apparently cooperating, Vaughn guides her every action. At the point of entry, Hassan provides a false code to the silo's alarm system. This activates an anti- intruder device and puts Sydney in grave danger as 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 scramble to get his guarantee, and Sydney returns to LA with the mysterious device.
Sydney and Vaughn visit CIA Director Devlin with the evidence about Jack. But they are stunned when Devlin and Jack, along with eight other senior officers, enter the room. And Jack reveals what most of them already knew...that he never was a KGB agent, but that it was Sydney’s mother...