Sydney`s search for her past leads to a jailed Sark, but their Q&A is cut short when he becomes the ransom for a pair of abducted CIA scientists, whose kidnappers may be tied to the murder of his father. Meanwhile, Jack contacts an old friend of sorts for info on Sloane`s new world-peace project; and Vaughn makes a decision about his future as an operative.
While trying to infiltrate a group bent on retrieving deadly biological weapons, Sydney discovers a link to her missing two years in the form of Simon Walker, the dangerous and sexy leader of the team. Meanwhile, Vaughn struggles with his own feelings of jealousy and longing while Sydney is on her mission, aware of the pressures his job is putting on his marriage to Lauren; and Jack takes matters into his own hands to protect his daughter, purposefully revealing Sydney`s deadly secret to Dixon in order to preserve her position inside the CIA.
Jack takes drastic measures to ensure that the NSC never finds out the truth about Sydney`s murder of a Russian diplomat. But his actions place a heavy strain on Vaughn`s marriage, as Lauren gets closer and closer to the truth about Sydney. Meanwhile, Sydney agrees to go on a mission with Sloane in order to thwart plans to obtain the operating system to a deadly weapon -- and she discovers an unlikely ally in the hunt for her missing two years.
Sydney and Vaughn must convince bomb maker Daniel Ryan that they are part of The Covenant in order to find out where he has hidden one of his devices. But Sydney discovers that her ties to the bomber could lead him on a suicide mission.
Sydney and Jack warn a disbelieving Vaughn about their suspicions of Lauren being the CIA mole. Meanwhile, Bomani and Sark take possession of the Rambaldi machine, Sydney and Vaughn must stop a Covenant virus that`s crippling medical facilities around the world, Sloane`s secret is revealed to Jack, and Bomani begins to lose faith in Lauren`s ability to carry out her Covenant missions.
After finding out that Lauren is working for the Covenant, Vaughn is told to keep up the fa?ade of a happy marriage in order to keep tabs on his wife`s activities. But he`s in for a shock when he uncovers the truth about Lauren`s mother, Olivia. Meanwhile, Jack refuses to help exonerate Sloane of his crimes and put in motion a stay of execution, and a monk discloses the identity of the Rambaldi "Passenger" to Sydney.
After discovering the identity of the Rambaldi "Passenger," Sydney and Jack seek the aid of Sloan, to track the "Passenger" down. Meanwhile, after learning a secret about his father from Thomas Brill, Vaughn is kidnapped and tortured by Lauren and Sark, who are hot on the trail of "The Passenger" themselves.