S03-E01 :: "The Two" :: Original Airdate: 09.28.03
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.
S03-E02 :: "Succession" :: Original Airdate: 10.05.03
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.
S03-E03 :: "Reunion" :: Original Airdate: 10.12.03
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.
S03-E04 :: "A Missing Link" :: Original Airdate: 10.19.03
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.
S03-E05 :: "Repercussions" :: Original Airdate: 10.26.03
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.
S03-E06 :: "The Nemesis" :: Original Airdate: 11.02.03
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.
S03-E07 :: "Prelude" :: Original Airdate: 11.09.03
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.
S03-E08 :: "Breaking Point" :: Original Airdate: 11.23.03
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. Meanwhile, Lauren faces an impossible choice -- side with the NSC, who she wants to believe is doing the right thing, or with her husband.
S03-E09 :: "Conscious" :: Original Airdate: 11.30.03
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.
S03-E10 :: "Remnants" :: Original Airdate: 12.07.03
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.
S03-E11 :: Full Disclosure :: Original Airdate: 01.11.04
The truth finally comes out about Syd's missing two years and the information comes from a most unlikely source.
S03-E12 :: Crossings :: Original Airdate: 01.18.04
Irina's sister names a steep price for helping Jack save Syd and Vaughn from a North Korean firing squad. Meanwhile, Sloane has no idea that it's his head on the line should Mr. Bristow cut a deal with his wicked sister-in-law.
S03-E13 :: After Six :: Original Airdate: 02.15.04
Murders among the Covenant lead Syd and Vaughn to a ghost from SD-6's violent past; a rogue security expert holds the key to a CIA technology breakthrough; Sark puts the screws to Lauren; Sloane's erratic behavior begins to trouble Jack; and Marshall freaks out after Carrie goes into labor.
S03-E14 :: Blowback :: Original Airdate: 03.07.04
Lauren's betrayal deepens as she and Sark sabotage Syd and Vaughn's mission to locate a bomb that could give the Covenant way too much power in the terrorist realm. Meanwhile, Sloane lures Barnett into an intimate exchange about the one sin that still haunts him.
S03-E15 :: Facade :: Original Airdate: 03.14.04
A bomb designer whose link to Sydney could lead to an explosive turn of events should he figure out that she and Vaughn are secretly posing as Covenant members.
S03-E16 :: Taken :: Original Airdate: 03.21.04
Syd wastes no time tracking down Sark after Dixon's kids go missing; Lauren finds a patsy to paint as the CIA mole to dupe her senator father, compelling Barnett to question everything she thought she knew about Sloane.
S03-E17 :: The Frame :: Original Airdate: 03.28.04
Syd leads the hunt for a Covenant honcho who could hold the key to a long-lost remnant of the Rambaldi puzzle; tragedy rocks Lauren's mother, while Jack's suspicions shock her father; and Vaughn makes a monumental decision about the future of his marriage.
S03-E18 Unveiled :: Original Airdate: 04.11.04
Bomani's cyber-attack to swipe international DNA records clues the CIA into just who the Covenant is trying to find; Jack seals Sloane's fate after learning about his affair with Irina; Vaughn refuses to accept the truth about Lauren, whose continued failures force Sark to make a deadly decision about his allegiances.
S03-E19 :: Hourglass :: Original Airdate: 04.18.04
Time runs out for Sloane, whose execution coincides with Syd and Vaughn's mission to snag a Rambaldi artifact that could reveal the Passenger and Lauren's realization that her cover has been blown iside the CIA. Meanwhile, Olivia orders Sark to abduct the monk who knows too much about the Bristows.
S03-E20 :: Blood Ties :: Original Airdate: 04.25.04
A ghostly Sloane teams with Syd and Jack to pump the Trust for an artifact that leads to his daughter, whose rescue reveals a family tie and a fatal lie. Meanwhile, Vaughn learns an awful truth about his father from a former ally and the evil lengths to which Lauren and Sark will go to locate the Passenger.
S03-E21 :: Legacy :: Original Airdate: 05.02.04
Toni Cummings and Irina's sister return to nail Sloane, who takes a risk of biblical proportions ‹ and cuts one hell of a deal ‹ to get the Rambaldi truth out of Nadia. Meanwhile, Vaughn's vendetta against Lauren turns deadly enough that Syd is forced to actually save the worst man she's ever encountered.
S03-E22 :: Resurrection :: Original Airdate: 05.23.04
Vaughn's crusade to bring down Lauren reaches critical mass, just as she hits a new low within the CIA; Syd makes a devastating find that tears her world apart; and Nadia is faced with the fact that her father may be the worst man on the planet.