Sydney and Jack are confronted by the new director of SD-6 who replaces Sloane, whose whereabouts and intentions are unknown. Meanwhile, romantic sparks begin to fly between Francie and Will.

Peyton tells Sloane that she has made a deal for the Rambaldi Sphere with an ally in China. Sloane arranges for stolen missiles to be sent to Hong Kong. Sloane's plan is revealed to the APO members, who race to stop him before he can use the Rambaldi Sphere to put the plan in motion. But this all leads to a long awaited confrontation between Sydney and Irina.

In order to save Will's life, Sydney and Vaughn must destroy a familiar looking Rambaldi device, while Jack makes a risky deal with Khasinau's representative, Mr. Sark. Meanwhile, the CIA believes that one of their own is a mole for "The Man"; the Alliance comes to a decision regarding the fate of Emily Sloane; Dixon's suspicions about Sydney intensify; and Sydney finds herself face-to-face with "The Man."

Sydney finally confronts her mother, who reveals her true motivation. Sloane, for his part, begins to execute his new grand plan and Will struggles to figure out who's behind his set-up.

Jack, Sydney, Irina, Vaughn and Nadia parachute into Sovogda. They're supposed to dismantle a giant red ball turning people into zombies. At APO, Marshall and Weiss use the Blackwell Index to blackmail the Russian minister into giving them the access codes to a Russian satellite, they discover that Elena is uplinking the satellite. A CIA agent, Brodien reminds them that the Rambaldi device is broadcasting a subaudible frequency that physiologically alters people who drink it and it is irreversible. Elena learns of the APO team's arrival.

Sydney finally learns the shocking truth about her missing two years from an unlikely source.

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.

While continuing on a mission to take control of six nuclear warheads, Sydney and Jack discover where Irina's loyalties lie when she meets up with Gerard Cuvee. Meanwhile, Sloane informs the Alliance that Emily may still be alive.

In the first part of [the] Alias two-hour finale event, 'Reprisal,' Sloane takes Marshall and Rachel hostage in order to discover a crucial clue to Rambaldi's ultimate endgame, as Sydney, Vaughn and APO race to stop him.

When a mission goes wrong, Sydney's is placed in danger and Marshall is the only one who can save her. Meanwhile, Dixon is exposed to a deadly pathogen released inside APO.

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.

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.

Vaughn disobeys orders and attempts to help Sydney and Jack avert the destruction of SD-6 headquarters and all its occupants. Meanwhile, McKenas Cole continues his vendetta against Sloane and searches for a mysterious device. A desperate but determined woman convince Will to continue his investigation of SD-6 and the imprisonment of David McNeil.

Sydney's loyalties are tested after a tragedy exposes the dark side of her superiors and the underhanded doings of her own father.

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

While Alliance counterintelligence head Ariana Kane tracks Sydney in order to catch her fugitive father, Jack elicits Irina's help in finding Sloane's blackmailer. Meanwhile, Sydney and Vaughn risk exposing their covers to SD-6 when they share a romantic dinner together while on a case in France.

Sydney defies her father in her attempt to rescue a kidnapped scientist, while Sloane, seeking revenge, becomes more dangerous than ever. Meanwhile, Francie manipulates an unsuspecting Will for his agency connections.

Will's life is about to change as he is sent to find the person responsible for leaking information to him about SD-6. Meanwhile, Sloane finds himself on the cusp of finally tracking down Khasinau when SD-6 captures "The Man's" right-hand man, Mr. Sark. Dixon becomes suspicious of Sydney's activities.

When armed intruders take over SD-6, led by McKenas Cole, a man bent on exacting revenge on ex-boss Sloane, Sydney and Jack must work together to save their colleagues. Meanwhile, Will fears that his investigation of SD-6 and its link to the murder of Eloise Kurtz is placing his life in jeopardy.

Rambaldi's catastrophic endgame begins to fall into place as a giant version of the Circumference/Mueller device is found floating over city in Russia, driving the citizens made. After a wounded Dixon reveals that Irina is alive, Sydney, Nadia, and Jack set off to find her. Irina had been captured, and then duplicated using Project Helix, in order to give the impression that she was dead. Sydney and Nadia discover Irina is being held inside a camp in Tikal, safely in the clutches of Elena's army. Irina had apparently been working to counter Elena's organization, the Covenant, and actually PREVENT the Rambaldi endgame. Irina tells of a page she destroyed, a page that was key to Rambaldi's endgame. Under torture, she finally broke and recreated it for Elena. After a short respite, the transport turns towards Russia, and Sydney, Vaughn, Jack, Nadia, and Irina parachute down, towards Elena, Sloane, the Circumference....and destiny.

Sydney and Vaughn go undercover as a married couple so as to find a weapon that could bring back the Dark Ages. However, the neighborhood they've infiltrated is not as charming as it seems.

Sydney begins to question Will's identity when he's arrested for espionage, under suspicion of being a double. Meanwhile Sark and Irina plot to recover the Rambaldi heart, and Sloane makes Jack a business proposal.

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.

Vaughn asks Sydney to use her friendship with Sloane's wife, Emily, to gain access to a mysterious Rambaldi book which happens to be under lock and key in a safe at Sloane's home. Meanwhile, Will is kidnapped and told to drop his investigation of SD-6 or risk the lives of his family and friends, including Sydney's.

Sydney faces off with her mother, while Emily must decide whether to side with her husband or betray him.

Jack's illness has caused him to hallucinate about a cure. Sydney must recreate the time when Jack was working for the CIA and hid the only man who might be able to help him now. For this, Sydney must play her own mother. Meanwhile, Sophia moves in with Sydney and Nadia.

Jack meets Alliance counterintelligence head Ariana Kane, who is sent in to investigate Emily's disappearance and to discover who is trying to blackmail Sloane. Meanwhile, Marshall is sent on his first mission with Sydney as his partner. Vaughn schedules Will to take a CIA psych test. Francie gets suspicious over Sydney and Will's secretive behavior.

The entire APO gang is trapped inside the CIA offices and Weiss saves them. However, Weiss will not be returning to APO, he will just be helping the others on a mission to obtain information regarding Sydney.

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.

Sydney races to find a cure for Vaughn, but in order to find the antidote, Sydney must make a deal with Sark that could endanger Sloane's life. Meanwhile, Will continues his research for Vaughn and discovers some disturbing inconsistencies involving 20-year-old standardized IQ tests.

Sydney is grateful and proud of her father after he saves her life while on a case in Havana. But her admiration is short lived when Vaughn discovers further evidence that Jack may have been responsible for the deaths of over a dozen CIA officers many years earlier.

Sydney now posing as Anna, brings Peyton a microchip with a device hidden in it. Meanwhile Sloane finishes translating page 47 and reports that only the chosen one can complete the circle, which leads Sark and Sydney on a dangerous mission to a prison. Rachel finally discovers Tom's secret about what happened to his wife.

After being infected with a hallucinogen, Sydney starts to lose touch with reality. Vaughn and Jack must rush to find an antidote before Sydney puts her life - and others next to her - into danger.

Sloane temporarily steps down as Director of his Task Force and gives Jack full authority over the next assignment, which involves Anna Espinosa, Sydney's old foe. However, Anna turns the tables on APO when she captures Nadia and forces Sydney to do her biddings. Sydney tells Nadia about the Rambaldi's prophecy which dictates that two sisters will fight and only one will survive. Meanwhile, Vaughn visits Sark and tries to trick him into helping them to catch Anna. In the end, one of the sisters is mortally wounded by Anna.

Nadia puts her own life - as well Sydney's and Weiss's - in danger after failing to unveil her past through a dangerous criminal. Meanwhile, Vaughn finds a person who is somehow connected to his father and Nadia as well.

Sydney and Tom discover that Renie has stolen the cryo container, and soon find themselves under siege by a group of mercanaries who want the contents of the container. Meanwhile, Sloane takes matters into his own hands to get himself back into APO.

While the gang starts to learn more about the Prophet 5, Sloane is distressed to learn that Prophet Five's cure for Nadia is just as likely to kill her. Meanwhile, Devlin returns, the search for Anna Espinosa continues, Rambaldi's prophetic Page 47 resurfaces, and Sydney offers Renée a job at APO.

Sydney quits the CIA and joins a Black Ops unit called "Authorized Personnel Only" alongside Dixon, Jack, Vaughn and... Sloane. Meanwhile, the truth Sydney found out in Wittenberg endangers her relationship with Jack, and eventually she reveals the awful truth to Vaughn.

Sydney and APO attempt to discover whom Gordon Dean is working for and what their end game is. Meanwhile, when the group claiming to have a cure for daughter Nadia continues to play mind games with him, Sloane struggles for control.

While on a case to track the activities of Khasinau, a.k.a. "The Man," Sydney runs into her ex-lover, Noah Hicks, who broke her heart and left without saying goodbye five years earlier. Meanwhile, Sydney tells Sloane that she wants to find her mother; Jack is ordered to see CIA psychiatrist Dr. Barnett to help him deal with his churning emotions after discovering that his wife may still be alive; and Will and Francie become suspicious of Sydney's activities after finding one of her airline ticket stubs.

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.

Sydney and Vaughn go undercover to track down a deadly new bio-weapon. Meanwhile, Sydney is concerned about Vaughn not having yet put Lauren behind, and Nadia turns to a Jack to find out the truth about her mother.

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 must seduce a murderous arms dealer in order to track down a stolen NSA code-breaker. Meanwhile, Vaughn fears for Weiss's life, and Sydney and Jack argue about telling Nadia the truth about her mother.

Sydney must protect the life of a civilian, whom she unintentionally put in danger. Meanwhile, Jack plans a visit with an old friend, and Vaughn uncovers more disturbing secrets about his father.

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 is forced to partner on a mission with new APO agent Thomas Grace. They discover that Rachel Gibson -- a spy suspected of being involved in activities against the U.S. -- has something shockingly in common with Sydney.

While the FBI detains and questions Sydney about her past and possible ties to a mysterious Rambaldi doomsday prophecy, Vaughn and Jack must race to free her and find a way to clear her name before her cover is blown and SD-6 is made aware of the situation. Once the rescue op has been launched, in her quest to prove her innocence, Sydney shocks even her usually unflappable father when she makes a chilling discovery that may unravel the mystery of the 500-year-old prophecy – she finds proof that Rambaldi's writings may hold more truth about an alleged weapon of mass destruction - and the fate of her own family.

Nadia's former caretaker, Sophia, has been severely beaten. She contacts Nadia and asks to meet her. Sloane is told by Sophia that she was beaten up, because someone is trying to track Nadia down, so he and Jack decide to tell their daughters the truth – Elena Derevko, the third and the most cruelest of the Derevko sisters, has been surveilling both Sydney and Nadia for a decade. Meanwhile, Jack's doctor advises him to tell Sydney about his illness.

While Sloane awaits the outcome of his sentencing, Sydney's life is put in grave danger when Gordon Dean discovers that Rachel is still alive.

Rachel receives a little help from Syd for her first solo mission while Sloan is back at APO in frequent contact with Gordon Dean.

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.

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.

In an attempt to talk to Sydney, Katya Derevko deliberately poisons herself and is temporally taken out from her cell. Once Nadia tells her sister about this, Sydney visits her aunt to tell her to stay away from Nadia. However, Katya unsettles Sydney by telling her that someone framed her mother as a means of getting her killed. Sydney sets off in search of the truth behind this story. Meanwhile, Vaughn becomes a rogue agent by getting involved with the people who might know his father's whereabouts. In the end, he and Sydney find out that the man behind these two plots is no other than A. Sloane. However, things are not exactly as they seem to be.

In order to catch Khasinau and get closer to finding her mother, Sydney and Vaughn set up an undercover transaction for a Rambaldi artifact with Khasinau's representative, Mr. Sark. But Sydney's cover may be compromised when a SD-6 agent is sent in to thwart the sale. Meanwhile, Will is enticed to continue his investigation of SD-6 when he learns the identity of one of his kidnappers. Emily tells Sydney that she knows about SD-6, which forces Sloane to make the most difficult decision of his life.

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 teams up with Renée - a fugitive on the CIA's most wanted list -- to track down the murderer of a close friend before the killer can strike again. Meanwhile, Jack enlists a reluctant new agent, Thomas Grace (Balthazar Getty), and Weiss struggles to decide whether or not to accept a promotion that would force him to leave his colleagues.

Sydney and Vaughn risk their lives trying to find out the truth about Vaughn's father. Finally, we find out why Jack and Sloane seem to be conspiring together against Sydney and Vaughn.

The team captures the Sloane Imposter and questions him to find a rare Rambaldi orchid. The real Sloane must relive a painful memory in order to get the Imposter to reveal the orchid location.

Dixon enlists Sydney to help him prove that Sloane is double-crossing the CIA and using APO to steal the Blackwell Index, a master blackmail list, and to reconstruct the Alliance. Sydney makes her way into Sloane's house so as to copy the encryption key from his secure phone and crack his calls. When Nadia finds her, she becomes disappointed in her sister. Meanwhile, Vaughn discovers something disturbing about his father when he visits his comatose uncle.

Sydney and Dixon are sent to Las Vegas to gather information from a K-Directorate agent who has ties to the group that attacked and nearly destroyed SD-6. Meanwhile, Sydney learns some shocking news about Francie's fiancé, Charlie, Will begins his journey in discovering what SD-6 really is, and Jack continues to try to be more of a father to Sydney when he helps her decide whether or not to continue with graduate school.

A Rambaldi artifact prophesizes that an apocalyptic event will soon take place, and Dixon's grief leads Vaughn and agency psychologist Dr. Barnett to question his intentions, as his thirst for revenge on Sloane intensifies. Meanwhile Sloane receives a life-changing revelation from a mysterious monk in Nepal, Sydney and Dixon hunt for the killer who stole the heart from his victim.

Sydney and Dixon go on a dangerous case involving the safety of the United Commerce Organization. Francie confronts Charlie about his secret date with another woman, and Will continues to get closer to the truth about Danny's murder.

After learning that the man she has known as Michael Vaughn is under investigation and suspected of being a double agent, Sydney begins to question whether their business and personal relationship over the years had all been a lie.