In this episode, Sydney finally learns the shocking truth about her missing two years from an unlikely source: FBI Special Officer Kendall. Kendall whisks her away and talks to her from the privacy of an airborne 757 jet. According to Kendall, Sydney was captured by the Covenant after her fight with Francie/Allison, held captive in Russia for over a year and brainwashed to become an assassin. But Sydney only pretended to be brainwashed and contacted Kendall who became her contact and handler, thus giving him information about the Covenant and about their quest for ...
Jack contacts a mysterious woman, that of former KGB agent Katya Derevko, Irina's older sister, to help him free Sydney and Vaughn, whose plane has crashed inside North Korea while seeking to find a defecting Russian scientist, named Leonid Lisenker, whom Sark is trying to kill before turning himself to the CIA. But Jack is faced with a curious conundrum when Katya tells him that she will not put the rescue plan in motion until he fulfills a favor: assassinate Sloane.
Sydney and Vaughn are sent to retrieve the Doleac Agenda to gain an advantage over The Covenant. For this, Sydney and Weiss must convince rogue security systems designer Toni Cummings to help the CIA break into a Lethal Response System. Meanwhile, Sark approaches an unlikely ally, that of Lauren Reed, to kill the Covenant's six cell leaders in order to take control of Covenant for themselves at the behest of the a senior leader, the rouge agent McKennis Cole.
While trying to retrieve a bomb, Sydney and Vaughn are ambushed by unidentified assailants. Meanwhile, Lauren and Sark continue to solidify their new partnership as the new leaders of the Covenant. Sloane divulges a dark secret to CIA therapist Dr. Judy Barnett about his past involving Sydney and Irina Derevko. Also, Marshall shows the strains of new fatherhood.
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 when she learns that Ryan's brother was the murder victim that she killed during her interment with the Covenant, and now Ryan wants revenge.
Sydney attempts to rescue Dixon's kids after they are kidnapped by Sark. Meanwhile, Lauren's status as a double agent for the CIA and the Covenant is put to the test when she learns that she has to work with her father; a wealthy U.S. Senator. When Laura's position is compromised, she and Sark decide to frame Sloane for being the CIA mole.
Sydney and Vaughn must track Kazari Bomani down to get hold of a piece of the Rambaldi puzzle before the Covenant gets their hands on it. Meanwhile, Jack reveals his suspicions to Senator Reed about his daughter Lauren's allegiances, and Vaughn decides what to do about his marriage.
Sydney and Jack warn a disbelieving Vaughn about their suspicions of Lauren being the CIA mole. Meanwhile, Kazari Bomani and Sark take possession of the Rambaldi machine as part of their greater master plan. Sydney and Vaughn must stop a Covenant virus that's crippling medical facilities around the world. Sloane's secret of being Sydney's biological father 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 really is working for the Covenant, Vaughn is told by Jack and Sydney to keep up the facade 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, whom is in league with her daughter over the Covenant's activities. 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 finally discovering the identity of the Rambaldi "Passenger," who is Sloane's illegitimate daughter, Sydney and Jack seek the aid of Sloane, to track the "Passenger" down, first by Sloane meeting with the five key members of a secret government group called "The Trust" to gain access to a Rambaldi device to locate the "Passenger". Sydney then travels to Chechnya to a prison where she finally finds her half-sister, Nadia Santos, an Argentine national and secret agent in hiding. Meanwhile, after learning a secret about his father from Thomas Brill, Vaughn is ...
With the aid of Katya Derevko and CIA imprisoned security systems designer Toni Cummings, Sydney and Vaughn attempt to track down Sloane and Nadia. But Lauren and Sark are also in hot pursuit of them in order to uncover the secrets of Rambaldi. Meanwhile, Vaughn's obsession with tracking down Lauren is beginning to consume him. During a mission to Cuba to uncover more Rimbaldi findings, Sydney and Vaughn turn the tables on an old foe; the Taiwanese scientist and torturer "suit and glasses. Also, Katya expresses her attraction to Jack.
Lauren stages a stunning betrayal by impersonating Sydney and blowing up the CIA offices to steal classified materials, and nearly killing Marshall in the process. But Sark is captured during Lauren's escape, and Sydney decides to play the impersonating game herself to learn where Laura is heading off too. Meanwhile, Vaughn comes face to face with his darkest demons in pursuit of his traitorous wife. Nadia must decide whether or not she can trust her father, Sloane, in the pursuit of Rambaldi's most priceless artifact and escape from CIA custody. During a mission to ...