Sydney tries to piece together the last two years of her life and discovers the fates of her friends and family. She confronts Vaughn about his marriage and learns the shocking fates of Jack and Sloane. Meanwhile, she is granted temporary CIA clearance on a case that may help her regain her memory.

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. 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.

Sydney and Vaughn are reunited again 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 familiar murderer. Sydney accompanies Vaughn and Lauren as they meet with Sloane to ask for a favor.

Sydney discovers a link to her missing two years in the form of Simon Walker, the dangerous and sexy leader of a group determined on retrieving deadly biological weapons. 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. 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, a kingpin in The Covenant; Jack's cover is jeopardized when he meets with Simon 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, Francie's doppelgänger, 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.

When Sydney is taken into custody by the NSC, Jack and Vaughn have no choice but to ally themselves with Sloane to rescue her. But with only hours to spare before she is forced to undergo a radical surgery to recover her memories, they must put togther an extraction team, headed by freelance operative Brill (Richard Roundtree, "Shaft"). Meanwhile, Lauren faces an impossible choice -- side with the NSC, who she wants to believe is doing the right thing, or with her husband.

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. Meanwhile, Lauren makes a great sacrifice in order to make her alibi believable to Lindsey after breaking Sydney out of NSC custody, and Sloane finds himself boxed in by an unlikely enemy -- one who wants to see Sydney Bristow eliminated permanently

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, Sloane, still under pressure from Lindsey, puts a plan in motion to eliminate Sydney, and Dr. Brezzel has an unpleasant run-in with Sark.

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.

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 to kill the Covenant's Cell leaders.

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.

Sydney attempts to rescue Dixon's kids after they are kidnapped by Sark, Lauren's status as a double agent is put to the test when she learns that she has to work with her father, and Sloane is framed as a CIA mole.

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 façade 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 Sloane, 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 about to track "The Passenger" down 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 them in order to uncover the secrets of Rambaldi. Meanwhile, Vaughn's obsession with tracking down Lauren is beginning to consume him, Sydney and Vaughn turn the tables on an old foe, and Katya expresses her attraction to Jack.