With no memory of her life during the past two years, Sydney struggles to come to grips with a reality that is both foreign and frightening. To begin her journey back, she confronts Vaughn about his marriage and the fact that he gave up hope of finding her. She also learns that Sloane weaseled his way into a formal pardon and an NSC honcho for locking Jack away on bogus charges. Sydney is granted temporary CIA clearance on a case that could be tied to her two-year disappearance and the recent murders of eight operatives.

Sydney, on the hunt for the truth behind her missing two years, confronts Sark, who is behind bars in CIA custody. But when a new terrorist organization, The Covenant, demands Sark in exchange for two scientists they've kidnapped, Sydney has to arrange a prisoner exchange against her will... only to discover a connection to her lost time. Meanwhile, Vaughn wrestles with the decision to return to the CIA even though it will mean working with Sydney, Jack confronts Sloane about Sloane's possible role in his daughter's disappearance — uncovering a surprising secret in the process — and Sydney meets Vaughn's wife.

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.

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.

Lauren senses Syd may be hiding something about Vaughn's stabbing, but must find a way to work with her husband's ex after Sloane is abducted by a Covenant bigwig. Meanwhile, Jack risks blowing his cover to grill Simon about Syd's lost two years; and Marshall is sent out on his second assignment where he has to impersonate a high-stakes 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.

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 memory, 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.

After making a shocking discovery in the desert, Sydney agrees to submit to an experimental procedure conducted by an eccentric doctor (David Cronenberg), 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.

Rating: 5.8/9

This episode was nominated for an Emmy award for Outstanding Cinematography for a Single-Camera Series. (Donald Thorin, Jr., Director of Photography)

The identity of the mysterious "St. Aidan" forces Sydney to pull a stunned Will (Bradley Cooper) out of witness protection. But the pursuit sends the two old friends on a collision course with Allison (Merrin Dungey) — 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 (David Cronenberg) has an unpleasant run-in with Sark. Written by Jeff Pinkner, directed by Jack Bender.

Rating: 5.4/8

Syd finally finds out where she spent her missing two years, and at the same time learns that Kendall is not FBI, but Special Research. It turns out Sydney was kindapped by The Convenant and brainwashed into thinking she was Julia Thorne. However, Sydney's training kept her from actually being turned, and she contacted Kendall 9 months into her brainwashing. It was Sydney herself that asked Kendall never to reveal to her what she did for those two years, because of the pain that those memories caused her. Kendall: Terry O'Quinn. Oleg: Bill Bolender. Lazarey: Mark Bramhall. Sark: David Anders.

Rating: 5.4/8

Jack contacts Irina's sister (Isabella Rossellini) 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. Leonid: Griffin Dunne. Col. Yu: Byron Chung. Zisman: Arnold Vosloo.

Upon discovering that high ranking members of The Covenant are being murdered, Sydney and Vaughn are sent to retrieve the Doleac Agenda — which contains operational plans for six of The Covenant's cells — to gain an advantage over the rogue assassins. But unbeknownst to all, a familiar force is at work orchestrating the reorganization of The Covenant. Meanwhile Sydney and Weiss go on a mission to convince rogue security systems designer Toni Cummings (Vivica A. Fox) to help the CIA break into a Lethal Response System, Sark presents a business proposal to Lauren, Jack urges a troubled Sloane to talk with CIA psychiatrist Dr. Judy Barnett (Patricia Wettig), and Marshall can't contain his excitement about becoming a father when Carrie goes into labor. Quentin Tarantino returns in a special guest appearance as McKenas Cole.

Rating: 5.6/8

In the episode — told through the eyes of Sydney and Vaughn and then reversed to see how the story unfolds through Lauren and Sark's perspective — Sydney and Vaughn are ambushed by unknown assailants while trying to retrieve a bomb. Meanwhile, Lauren and Sark continue to solidify their new partnership, Sloane divulges a dark secret to Dr. Barnett (Patricia Wettig) and Marshall shows the strains of new fatherhood. Written by Laurence Andries, directed by Lawrence Trilling.

Rating: 4.7/7

Sydney and Vaughn must convince bomb maker Daniel Ryan (Ricky Gervais) 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. Lisenker: Griffin Dunne. Written by R.P. Gaborno & Christopher Hollier, directed by Jack Bender.

Rating: 4.8/7

When Dixon's children are kidnapped by Sark, he turns to Sydney in a desperate attempt to rescue them. Meanwhile, Lauren's work as a double agent comes under intense pressure when her estranged 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 (Patricia Wettig) into the crossfire.

Rating: 4.9/7

This episode was nominated for an Emmy award for Outstanding Art Direction for a Single-Camera Series. (Scott Chambliss, Production Designer, Cecele DeStefano, Art Director and Karen Manthey, Set Decorator)

Sydney and Vaughn are in hot pursuit of Covenant kingpin Kazari Bomani (Djimon Hounsou) to track down an important piece of the Rambaldi puzzle. Meanwhile, Jack discloses his suspicions to Senator Reed about his daughter Lauren's allegiances, Lauren's mother (Peggy Lipton) is faced with a tragedy, and Vaughn decides the fate of his marriage.

Rating: 5.3/8

Sydney and Jack warn a disbelieving Vaughn about their suspicions of Lauren being the CIA mole. Meanwhile, Bomani (Djimon Hounsou) 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.

Rating: 5.3/9

This episode was nominated for an Emmy award for Outstanding Hairstyling for a Series. (Michael Reitz, Department Head Hairstylist, Karen Bartek, Key Hairstylist, Grace Hernandez, Hairstylist, and Julie Woods, Hairstylist)

After discovering that Lauren is working for the Covenant, a betrayed Vaughn is told to keep up the facade of martial bliss 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 (Peggy Lipton). Meanwhile, Jack refuses to help exonerate Sloane of his crimes and put in motion a stay of execution, and a monk (David Carradine) -- faithful to the study of Rambaldi -- discloses the identity of the Rambaldi "Passenger" to a stunned Sydney. Guest starring Jimmy Bridges as DOJ agent, David Carradine as Conrad, Peggy Lipton as Olivia Reed, Glenn Morshower as Agent Bell, and Patricia Wettig as Dr. Judy Barnett. Written by Josh Appelbaum & André Nemec, directed by Ken Olin.

Rating: 5.2/8

This episode was nominated for an Emmy award for Outstanding Single-Camera Sound Mixing for a Series. (Robert Appere, Re-Recording Mixer, Edward Carr III, Re-Recording Mixer and Douglas Axtel, Production Sound Mixer)

After discovering that the Rambaldi "Passenger" is Sydney's half-sister, Nadia (Mia Maestro) — by way of Irina — Sydney and Jack seek the aid of Nadia's father, Sloane, to track her down. Meanwhile, after learning a secret about his father from Thomas Brill (Richard Roundtree), Vaughn is kidnapped and tortured by Lauren and Sark, who are hot on the trail of "The Passenger" themselves. Guest starring Mia Maestro, Richard Roundtree, Glenn Morshower, Yun Choi, Erik Jensen, and Donna M. Perkins. Teleplay by J.R. Orci, story by Alison Schapker & Monica Breen, directed by Jack Bender.

Rating: 5.2/8

With the aid of Katya Derevko (Isabella Rossellini) and CIA imprisoned security systems designer Toni Cummings (Vivica A. Fox), Sydney and Vaughn attempt to track down Sloane and his daughter, Nadia (Mia Maestro) - Sydney's half-sister. But Lauren and Sark are also in hot pursuit of Sloane and Nadia 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. Written by Jesse Alexander, directed by Lawrence Trilling.

Rating: 5.4/8

Season finale

Lauren stages a stunning betrayal to steal classified materials from the CIA. Vaughn comes face to face with his darkest demons in pursuit of his wife. Nadia (Mia Maestro) must decide whether or not she can trust her father, Sloane, in the pursuit of Rambaldi's most priceless artifact. Sydney receives a shattering revelation that will make her question everything - and everyone - she thought she could trust. Isabella Rossellini guest stars as Katya Derevko. Written by Jeff Pinkner, directed by Ken Olin.

Rating: 5.1/8

This episode was nominated for two Emmy awards. One for Outstanding Sound Editing for a Series (Thomas E. de Gorter, M.P.S.E., Supervising Sound Editor, Christopher Reeves, M.P.S.E., Sound Editor, Mark Allen, M.P.S.E., Sound Editor, Steven M. Davis, Music Editor, Pat Cabral, Foley Artist, and Cynthia Merril, Foley Artist) and one for Outstanding Stunt Coordination (Jeff Habberstad, Stunt Coordinator).