Having woken up in Hong Kong, with no memory for the last two years (!), Sydney returns to Los Angeles to try to piece together the last two years of her life and discovers the fates of her friends and family: Vaughn has married thinking that Sydney was long dead; Marshall is having a baby with CIA tech expert Carrie Bowman; and Dixon is now the new division head of the L.A. office branch of the CIA. Sydney also learns the shocking fates of Jack and Sloane; the former is in CIA custody for communicating with Irina whom still is in hiding, while the latter is living in Switzerland under house arrest in exchange for co-operation with the CIA. Sydney is granted temporary CIA clearance on a case that may help her regain her memory and she meets a new enemy group called The Covenant.

Sydney's search for her past leads to an imprisoned Sark, but their Q&A is cut short when he becomes the ransom for a pair of abducted CIA scientists by the Covenant, 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 in Switzerland. Also, Vaughn makes a decision about his future as an operative for the CIA.

Sydney and Vaughn are reunited again as a team to prevent Sark, now a head leader of the Covenant, from destroying the nation's satellite communications system. Meanwhile, Jack must find a way to stop Marshall from uncovering the identity of a murderer suspect whom is Sydney. Also, Sydney accompanies Vaughn and his wife, 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 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, and purposefully revealing Sydney's deadly secret of being a brainwashed assassin for the Covenant during her two-year absence 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. Also, Marshall is sent on his second mission with Sydney, posing as a high-stakes, southern-accented gambler.

Sydney's emotions are turned inside-out when she once again comes face-to-face with Allison Doren, the murdered Francie's doppelgänger, who was presumed dead but is now a key assassin working for the Covenant. Meanwhile Lauren's search for Lazarey's murderer leads her closer to discovering the 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 the Russian diplomat Lazarey. 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 honcho Mr. Lindsey, 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 together an extraction team, headed by freelance operative Brill. Meanwhile, Lauren faces an impossible choice: side with the NSC who she wants to believe is doing the right thing, or with her husband in their rescue of Sydney.

After making a shocking discovery of a severed human hand in the desert that belonged to Lazarey, the Russian diplomat she murdered while working as a brainwashed assassin for the Covenant, and who may in fact be alive, Sydney agrees to submit to an experimental procedure conducted by an eccentric doctor, named Dr. Brezzel, 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 of allowing herself to get tortured and beaten up in order to make her alibi believable to Lindsey after helping breaking Sydney out of NSC custody. Also Sloane finds himself boxed in by an unlikely enemy, that of Mr. Lindsey, who wants to see Sydney Bristow eliminated permanently.

The identity of the mysterious "St. Aidan" forces Sydney to pull a stunned Will Tippin out of witness protection for help in finding Lazarey to clear her name. But the pursuit sends the two old friends on a collision course with Allison, the Francie impostor who ruined both their lives. Meanwhile, a jealous 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 whom is also looking for Sydney.

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 Rambaldi artifacts. Sydney also staged the murder of Andrian Lazarey, and then deliberately had her memory erased to prevent the Covenant from knowing about secrets she had learned about Rambaldi's findings.

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.

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 kidnapped and tortured by Lauren and Sark, who are about to track "The Passenger" down themselves while Dixon, Weiss and Marshall race against the clock to find Vaughn before he is killed.

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 South Africa at a Rimbaldi artifact dig, Sydney has a some help and hindrance from Katya Derevko, as well as a final one-on-one fight with Lauren. Afterwards, Sydney receives a shattering revelation from Lauren that will make her question everything (and everyone) she thought she could trust.