||Upon mysteriously awakening in Hong Kong after fighting with doppelganger Francie in Los Angeles, Sydney learned that two years had passed and everyone presumed she was dead... and she has no recollection of those years. Returning to the world that she once knew will turn out to be both enlightening and painful, as Sydney searches to discover where she has been and what had transpired during the missing time.
||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.
||For the first time in two years, Sydney and Vaughn are reunited as a team to prevent Sark from destroying the nation`s satellite communications system. Meanwhile, Jack must find a way to stop Marshall from uncovering the identity of a murderer, and a suspicious Sydney accompanies Vaughn and Lauren as they meet with Sloane to ask for a favor.
||A Missing Link
||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.
||While Vaughn`s life hangs in the balance, Lauren butts heads with Sydney after learning the part she played in his stabbing. Meanwhile, Sydney further questions Sloane`s allegiances after he is kidnapped by Kazari Bomani (Djimon Hounsou), a kingpin in The Covenant; Jack`s cover is jeopardized when he meets with Simon (Justin Theroux) to dig up information on Sydney`s missing two years; and Marshall is sent on his second mission with Sydney, posing as a high-stakes, southern gambler.
||Sydney`s emotions are turned inside-out when she comes face-to-face with Allison ? a.k.a. doppelganger Francie ? who was presumed dead but is now a key figure in The Covenant. Meanwhile Lauren`s search for Lazarey`s murderer leads her closer to discovering a connection to Sydney, and Sydney begrudgingly is assigned as Sloane`s CIA handler.
||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.
||Now in Lindsey`s custody, Sydney is imprisoned and tortured at Camp Williams, a secret NSC detention facility. She befriends Campbell, another prisoner. Lindsey relieves Dixon, who takes full responsibility for hiding Syd`s secret. Lindsey pressures Lauren, who`s unaware of Syd`s torture, to write a fair report of their treatment of Syd.
||After making a shocking discovery in the desert, Sydney agrees to submit to an experimental procedure conducted by an eccentric doctor, designed to retrieve her lost memories. But while Jack and Vaughn look on, Sydney`s mind proves surprisingly resistant to letting her remember her missing time -- and the process of recovering it could end up killing her.
||The identity of the mysterious "St. Aidan" forces Sydney to pull a stunned Will out of witness protection. But the pursuit sends the two old friends on a collision course with Allison -- the woman who ruined both their lives. Meanwhile, a zealous Lindsey arrests Jack and Vaughn as conspirators in Sydney`s escape from NSC custody.
||Sydney finally learns the shocking truth about her missing two years from an unlikely source.
||Jack contacts a mysterious woman with ties to Irina to help him free Sydney and Vaughn, who have been captured and face a North Korean firing squad. But Jack is faced with a curious conundrum when the woman tells him that she will not put the rescue plan in motion until he fulfills a favor - assassinate Sloane.
||Upon discovering that high ranking members of The Covenant are being murdered, Sydney and Vaughn are sent to retrieve the Doleac Agenda to gain an advantage over the rogue assassins.
||While trying to retrieve a bomb, Sydney and Vaughn are ambushed by unidentified assailants. Meanwhile, Lauren and Sark continue to solidify their new partnership, Sloane divulges a dark secret to Dr. Barnett and 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.
||Dixon pleads Sydney to help him rescuing his children that were kidnapped by Sark. Meanwhile, Lauren`s work as a double agent is compromised when her father, Senator Reed, shuts her out of intelligence briefings. But she proves her worth when she frames Sloane as the mole inside the CIA-bringing his relationship with Dr. Barnett into the crossfire.
||Sydney and Vaughn must track Kazari Bomani down to get hold of a piece of the Rambaldi puzzle. 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, 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.
||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 Sloane and Nadia in order to uncover the secrets of Rambaldi.
||Sydney strategically places cell phones throughout the office. She patches into the CIA computer and downloads the Rambaldi equation. Then she contacts Sark - Sydney is actually Lauren in disguise! She shoots Marshall when he questions her. As she bolts, the cell phones explode.