Sydney confronts the enigma that represents not remembering anything from the last two years of her life and what has happened to her friends and relatives in the meantime. She confronts Vaughn, who has married someone else because he believed Sydney was dead. Sydney also learns that her father, Jack Bristow, has been imprisoned and isolated and that Arvin Sloane is a new man working as CEO for a philanthropic organization called Omnifam. Meanwhile, she is granted temporary CIA clearance on a case that may help her regain her memory.

International titles

• German: 2 Jahre (2 years)
• French: Les deux (The two)
• Polish: Dwa lata później (Two years later)

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.

The episode shows a CIA plaque with names of "agents killed in action" which includes below "Bristow Sydney A." the name of production designer Scott Chambliss.

International titles

• German: Erbfolge (Succession)
• French: Succession
• Polish: Sukcesja (Succession)

Sydney and Vaughn are reunited again as a team to prevent Sark from destroying the nation's satellite communications system. Meanwhile, Jack Bristow 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.

International titles

• German: Medusa
• French: Arme secrète (Secret weapon)
• Polish: Jak za dawnych lat (Just like in the old days)

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, purposely revealing Sydney's deadly secret to Dixon in order to preserve her position inside the CIA.

International titles

• German: Unbekannter Liebhaber (Unknown Lover)
• French: Chaînon manquant (Missing link)
• Polish: Brakujące ogniwo (Missing link)

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.

International titles

• German: Messerstiche (Stabs)
• French: Black Jack
• Polish: Konsekwencje (Consequences)

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 Andrian Lazarey's murderer leads her closer to discovering a connection to Sydney, and Sydney begrudgingly is assigned as Sloane's CIA handler.

International titles

• German: Feindinnen (Enemies)
• French: Noir et blanc (Black and white)
• Polish: Nemezis (Nemesis)

Sydney accompanies Sloane on a Covenant assignment to steal the operating system for a microwave laser from the Chinese Defense Minister's office. Marshall uses a camouflaged remote-control car to disable security, allowing Sydney to break into a safe. When discovered by security, Sydney overpowers two guards, scrambles the operating system and escapes. Sloane then gives Sydney an envelope written in Sydney's handwriting, containing a key and a coded message ("34-14, 09-55/9, 23-185, 17-15/3") that points to an apartment in Rome. Jack explains that the message was encoded in a scheme used by Sydney's mother, suggesting that they were in contact during Sydney's two-year disappearance.

Meanwhile, Vaughn and Lauren go to Mexico to meet Javier Perez, one of Simon Walker's former associates, who was captured by Mexican police and who claims to have information about Lazarey's murder. They are taken hostage en route, giving Jack a chance to kill Perez and make it appear as a suicide. However, Sark later finds Lauren and provides evidence that Julia Thorne is really Sydney and that she killed Lazarey. Sark claims to be interested in avenging his father's death.

Vaughn helps Sydney escape before being arrested by the National Security Council and Lauren tells Dixon that he is no longer in charge of the task force due to his hiding of evidence concerning Lazarey's murder.

The episode ends with Sydney entering the apartment in Rome. She recognizes a nearby statue as a recurring feature in her nightmares but is suddenly arrested by police.

International titles

• German: Alpträume (Nightmares)
• French: Sans issue (Dead end)
• Polish: Preludium (Prelude)

The National Security Council assumes control of the Task Force, with Lindsey replacing Dixon. Sydney is taken to Camp Williams, an NSC detention center used for interrogation of terrorists, and is subjected to shock therapy to coerce her into decoding a message found in her Rome apartment. Her attempt to escape fails.

Jack and Vaughn organize a rescue team with help from Sloane. They obtain blueprints of Camp Williams by infiltrating a Federal Emergency Managementfacility but Sloane is shot in the escape. Jack operates on Sloane to remove the bullet.

Lindsey blackmails Vaughn's wife, Lauren, into filing a false report on Sydney's interrogation under the threat of blackmail regarding Vaughn's involvement in Sydney's earlier escape.

Sydney is persuaded to reveal the contents of the message when a fellow inmate is tortured. However, the inmate is then revealed to be working for the NSC, who know that empathetic suffering is harder for Sydney to sustain than physical torture.

Marshall attempts to obtain access codes for Camp Williams, but they have mysteriously been deleted. With Lauren's help, the extraction team infiltrate the Camp just as Dr Vasson is about to fatally operate on Sydney to obtain information about her missing two years. Lauren helps them rescue Sydney, who reveals that she gave fake coordinates to Lindsey.

Notes

• Pruitt Taylor Vince guest stars as Campbell / Schapker
• The inmate's name is Schapker, the name of an Alias writer.

International titles

• German: Bis an die Grenzen (To The Limit)
• French: Volte-face (Volteface)
• Polish: Punkt kulminacyjny (The climax)

Sydney and Jack visit the co-ordinates from the coded message and find a box containing the hand of a Rambaldi follower. Lauren returns to the CIA, claiming to have been captured by The Covenant who are asking for the Rambaldi Device in exchange for Sydney.

Sydney visits Dr Brezzel, a neuro-researcher who specializes in dream memory state. Sydney is put into a drug-induced dream state and awakens in an ambulance with Vaughn watching over her. Vaughn explains that Will is going to be okay and that Francie was really Alison Doren. Sydney realizes that she is in the past and that Vaughn isn't married.

Suddenly, Vaughn changes into Sloane, who tells Sydney that she is dreaming. He then pushes her back to her apartment, representing her last memory before her amnesia. She enters her own dream and witnesses herself being taken away. Suddenly, she is experiencing her seventh birthday party, and the name St Aidan is on the cake. Lazarey appears and Sydney cuts off his hand instead of the cake.

Sydney then enters a building where her unconscious body is taken inside doors marked with the number 47. She meets Lauren, who then attacks her. Sydney says "You were part of this" but then suffers a heart failure in real life. She is resuscitated by the Doctor.

Lindsey meets Sloane, who claims to have confirmation of The Covenant's involvement in Sydney's capture. Lindsey asks Sloane for an assassin who can kill Sydney during the exchange. Lindsey shows Sloane proof that he knows Sloane's endgame.

Lauren matches the DNA from the hand with Lazarey, but the hand was alive only four months ago, so Sydney did not kill Lazarey.

Sydney enters the dream state again and is in a car with Dixon. The name St Aidan appears again. Sydney meets herself in her dream and her alternate self tells her to trust Lazarey. They fight each other and Sydney shoots herself. She enters Room 47 and utters "Oh my god!".

International titles

• German: Bei Bewusstsein (Conscious)
• French: Salle 47 (Room 47)
• Polish: Odmienne stany świadomości (Altered states of consciousness)

In her dream, Sydney sees Will and the name St Aidan. She visits Will who is now working as a construction foreman. He had thought Sydney was dead but Sydney proves her identity and tells Will that Alison Doren is still alive, working for The Covenant. Will explains that St Aidan is the name of a contact he had while with the CIA.

Sydney and Will meet St Aidan, who is really Andrian Lazarey with one hand missing. Sark appears, manages to kidnap Lazarey and tortures him for information.

Will and Sydney reminisce and become intimate. Sydney finds information that she may have a safe deposit box in an Austrian hotel in Graz. She goes there with Will and they break into a safe deposit box under the name of Julia Thorne. However, Sark gets there first and steals a metal cube. Will fights and kills Allison Doren and Sydney gets the cube back from Sark. The Rambaldi Cube contains a sample of human tissue, still active, bearing the name Milo Rambaldi.

Lindsey suspects that Jack and Vaughn know Sydney's location and arrests them. He arranges for Sloane to hire an assassin to kill Sydney when she gets exchanged for a Rambaldi device, threatening to reveal Sloane's extra curricular activities to the Justice Department. However, Sloane actually has Lindsey killed and steals the Rambaldi device for himself.

Note

• Bradley Cooper guest stars as Will Tippin.
• Merrin Dungey guest stars as Allison Doren.

International titles

• German: Überreste (Remnants)
• French: Jeu de piste (Treasure hunt)
• Polish: W obliczu śmierci (In the eyes of death)

During the recap, Rambaldi's prophecy is repeated: "This woman here depicted will possess unseen marks, signs that she will be the one to bring forth my works. At vulgar cost this woman will render the greatest power unto utter desolation."

The Rambaldi Cube is taken by the Department for Special Research but is hijacked by The Covenant. Sydney is kidnapped by FBI Assistant Director Kendall, who admits that he knows what happened during Sydney's missing years but had not revealed this information because Sydney had requested him not to do so.

Kendall explains that Sydney was believed to have died and they had found remains of a body matching her DNA. Nine months later, Kendall had received a call from Sydney who had just escaped from The Covenant and wanted to return. Sydney met with Kendall and told her story. After shooting Alison Doren, Sydney had awoken in a van, with her mouth taped and held captive by a man named Oleg. Together they watched Sydney's memorial service. Oleg explained that Alison Doren had been replaced with Francie's body and that Sydney's death had been faked by extracting pulp from her teeth and injecting it into her replacement corpse before burning it.

Sydney recognizes Oleg as the man she killed in Hong Kong a week after waking up.

Kendall explains that Sydney was taken to a Covenant facility, spent six months being brainwashed and murdered a man as a test of loyalty. However, Kendall explains that, as a child, Sydney had been a part of Project Christmas, a CIA program to train and prepare children for intelligence work. The program contains a failsafe to prevent subjects from being turned. This gave her the ability to withstand brainwashing.

Sydney had wanted to escape The Covenant, but Kendall had persuaded her to return, lest her friends and family be at risk. Sydney resumed the role of Julia Thorne, keeping Kendall informed of her activities. The Covenant had wanted Sydney to obtain information about the Rambaldi cube from Lazarey and then kill him. Instead, Sydney helped fake Lazarey's death.

Kendall explains that he has always been working for Special Research, collecting Rambaldi artifacts and that Sydney is still believed to be The Chosen One. The Covenant had wanted both Sydney and the Cube to fulfill Rambaldi's prophecy. Sydney tracked down the Cube to a cave in Namibia, where Lazarey used 12 keys he had collected over 30 years. However, Sydney had to amputate Lazarey's hand, which had become trapped. Kendall had then received a DVD where Sydney explains that she is going to have her memory of the past two years erased so that the location of Rambaldi's DNA can be kept a secret. She also asked Kendall to keep this information secret from herself if she returns.

Kendall explains that followers of Rambaldi's prophecy believe that Rambaldi's DNA can be used to fertilize the egg of a surrogate mother, who is referenced in his prophecy as The Chosen One. Sydney then looks down at a scar on her abdomen and realizes that her eggs had been stolen and that Rambaldi's child would also be her own.

A mission is mounted to retrieve the Cube, which Marshall had secretly tracked. Dixon accompanies them, revealing that he had also known the truth about Sydney's disappearance. They enter the building, overcome opposition and Sydney, against Kendall's orders, burns the equipment and the test tubes bearing her name. They find Lazarey, but Sark escapes and transmits a message telling someone to take care of his father. Lazarey asks Sydney if she knows about The Passenger but is then killed by a sniper. The sniper is Vaughn's wife, Lauren.

Guest voice star: Quentin Tarantino

International titles

• German: Enthüllungen (Revelations)
• French: Passé recomposé (Reconstructed past)
• Polish: Ściśle tajne (Top secret/Strictly confidential)

Sydney and Vaughn travel to North Korea to meet with a Covenant defector. Lauren passes this information to The Covenant, who then poison the pilots. En route, the pilots die, Sydney and Vaughn evade North Korean missile attacks, crash land the plane and elude the military.

Sydney and Vaughn discuss the difficulty of working together. Sydney reveals that she had slept with Will and has decided to move on. Before Sydney and Vaughn can meet the defector, Sark appears and masquerades as a CIA operative. Sydney, Vaughn and the defector are captured by the military but Sark escapes. The defector informs on Sydney and Vaughn, who are then physically abused.

Jack contacts Sydney's mother, Irina Derevko, for assistance and is visited by Irina's sister, Katya, who offers help in exchange for Sloane being killed. Jack visits Sloane but Katya first calls Sloane and warns him to back off Irina, hinting that even Jack would turn against him. Katya then contacts Jack and aborts the assassination.

Vaughn admits his feelings for Sydney before they are taken to a firing squad. Instead of being killed, one of the guards kills the other soldiers and they all escape with the defector.

Notes

• Isabella Rossellini guest stars as Katya Derevko.
• Griffin Dunne guest stars as Leonid Lisenker.

International titles

• German: Überläufer (Defector)
• French: Ennemi intérieur (Inner foe)
• Polish: Na rozdrożu (At the crossroads)

The Covenant defector, Lisenker, discloses the location of the Doleac Agenda, a microdisc which contains information about the six Covenant cells. It is in a chalet with a protection system designed by security expert Toni Cummings, whom Sydney and Weiss meet while posing as diamond smugglers. They obtain schematics of the security systems, bypass the lethal response security and escape with the Agenda.

Sloane meets with CIA psychologist Dr. Barnett and reveals that he has a secret that affects the only two people he cares about in the world, Sydney and Jack.

Sark meets with Lauren and reveals that he knows her affiliation with The Covenant. He proposes that they stage a coup, kill all six cell leaders and demand ascension within The Covenant by threatening to present the CIA with access keys kept by each of the leaders. After killing the leaders, Sark meets with McKenas Cole who then reveals that Lauren had informed him of their intentions and was happy that the leaders were dead since the CIA were soon to learn of their identities. As a reward, Cole makes Sark and Lauren the heads of the North American cell.

Notes

• Quentin Tarantino guest stars as McKenas Cole.
• Vivica A. Fox guest stars as Toni Cummings.

International titles

• German: Neue Allianzen (New Alliances)
• French: Nid d'aigle (Eyrie)
• Polish: Do sześciu razy sztuka (Sixth time lucky)

The CIA intercepts a communication suggesting that a terrorist organization, Shining Sword, has a plasma charge weapon. Sydney and Vaughn access a secure data facility to download information but their access is cut short by a Covenant operative who escapes after a car chase. They trace the weapon to a ship but Vaughn is shot while on board.

The story is then replayed, with additional scenes showing Lauren's involvement in the operation. She had leaked information, it was her in the secure data facility and it was she and Sark that had escaped in the car. Lauren is aroused by the operation and makes love with Sark.

Back aboard the ship, Sark and Lauren attempt to stop Sydney and Vaughn. Vaughn gets the upper hand, demanding that Lauren remove her mask but before Lauren reveals her identity, Sark threatens to kill Sydney. Sark and Lauren escape, arming the weapon which Vaughn disables with Marshall's remote assistance.

Sloane meets Dr. Barnett, revealing that he had an affair with Irina Derevko and that Sydney may be his daughter.

International titles

• German: Rückschlag (Blowback)
• French: Duel masqué (Disguised duel)
• Polish: Para za parą (Pair follows pair)

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.

Daniel Ryan, former bomb disposal expert, has created a bomb and detonates it in public to advertise his skills and prove that the bomb cannot be disarmed. He is willing to sell the bomb to The Covenant. Based on information from Lysanker, the CIA captures Ryan, under the guise of representing The Covenant.

They reproduce a Moscow hotel in order to convince Ryan that he is dealing with The Covenant. Ryan agrees to the deal, but demands that the information be provided only to Sark on a scheduled airline flight. When the contact does not eventuate, the CIA investigates Ryan and discovers that The Covenant had killed his brother. It was Sydney who had performed the murder, during a test of loyalty (explained in Full Disclosure, episode 11). A bomb is then discovered on board the plane carrying Vaughn and Sark which will activate if the plane descends to land.

The CIA reveal their identity to Ryan but he refuses to help. Sydney sympathizes with Ryan, explaining that The Covenant also stole a part of her life when turning her into Julia Thorne. Ryan then agrees to disarm the bomb, supplying a pager code. However, this actually activates the timer of the bomb on board the plane, together with one held in the CIA office, with only 5 minutes until detonation. Ryan explains that he knows it was Julia Thorne who killed his brother.

Jack manages to coerce Ryan into providing a deactivation code and both bombs are stopped with one second remaining.

Notes

• Ricky Gervais guest stars as Daniel Ryan.
• Griffin Dunne guest stars as Leonid Lisenker.
• This episode substitutes an establishing shot of Cork City for Belfast.

International titles

• German: Späte Rache (Late Revenge)
• French: Sueurs froides (Cold sweat)
• Polish: Za fasadą (Behind the facade)

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.

International titles

• German: Artefakt 45 (Artifact 45)
• French: Trou noir (Black hole)
• Polish: Porwanie (Kidnapping)

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.

International titles

• German: Sündenbock (Scapegoat)
• French: Le passager (The passenger)
• Polish: Szpieg, który mnie okłamał (The spy who lied me)

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 computer 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.

International titles

• German: Enttarnt (Unmasked)
• French: Il Dire
• Polish: Niewierna (Unfaithful)

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.

International titles

• German: Stundenglas (Hourglass)
• French: Compte à rebours (Countdown)
• Polish: Poszukiwacze zaginionego pasażera (Lost passenger prospectors)

After discovering the identity of the Rambaldi "Passenger," Sydney and Jack seek the aid of Sloane, to track the "Passenger" down, which involves infiltrating a museum, using retinal scans (obtained by Arvin Sloane) from the members of The Trust. 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.

International titles

• German: Blutsbande (Blood Ties)
• French: Protocole Enfer (Protocol Hell)
• Polish: Więzy krwi (Blood ties)

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.

Note

• Isabella Rossellini guest stars as Katya Derevko.
• Vivica A. Fox guest stars as Toni Cummings.

International titles

• German: Vermächtnis (Legacy)
• French: Traque infernale (Infernal hunt)
• Polish: Dziedzictwo (Legacy)

Lauren stages a stunning betrayal to steal classified materials from the CIA. Meanwhile, Vaughn comes face to face with his darkest demons in pursuit of his wife; Nadia must decide whether or not she can trust her father, Sloane, in the pursuit of Rambaldi's most priceless artifact; and Sydney receives a shattering revelation that will make her question everything - and everyone - she thought she could trust.

Note

• Isabella Rossellini guest stars as Katya Derevko.

International titles

• German: Auferstehung (Resurrection)
• French: Objectif ultime (Ultimate goal)
• Bulgarian: Наричана Още:Развръзка (Resurrection)
• Polish: Odrodzenie (Resurrection/Revival)