When Sydney learns that Marshall has been kidnapped, she struggles against a heartless Sloane to bring Marshall back whom is being tortured by the same Taiwanese torturer Dr. Lee "Suite and Glasses" to uncover the code for the top secret ECHELON security system whom tries to stall for time. Sydney and Dixon are instead sent to Ho Chi Minh City, Vietnam to recover the hard drive for ECHELON. Meanwhile, Kendall and the rest of the CIA frantically tries to prevent SD-6 from gaining access to ECHELON... and Jack realizes that the only one who can help them is Irina.
Sydney and Vaughn reach a crossroads as they try to turn a professional relationship into a personal one during a mission to recover an experimental gyroscope. Meanwhile, Jack struggles to outwit the persistent SD-6 security expert, Ariana Kane, as she tightens the noose of suspicion around him of being Sloan's blackmailer. But Sloan is eventually revealed to know more than he claims: there never was a blackmailer, and Emily is really alive and in league with Sloan to get away from the Alliance!
In this episode, the entire world of 'ALIAS' is turned upside down, beginning with the mysterious disappearance of Sloane that brings Anthony Geiger, the new head of SD-6 into Jack and Sydney's life. As the Bristows struggle to stay one step ahead of having their secret blown wide open by Geiger, Will and Francie make a startling discovery of their own as she prepares to open her new restaurant. After an airborne mission to recover something called a Server 47 dive, Sydney uncovers a crucial weakness, one that could bring down the entire Alliance. But to put her plan ...
When a young CIA agent dies, suspicion immediately falls on her parter and lover, agent Jim Lennox. But after Sydney rescues Lennox from captivity, She trikes up an instant connection as they discover shared wounds - realizing They've both lost someone they love to the job. Yet even her judgment is thrown when Vaughn and Jack discover that Lennox was pursing a technology that allows people to change their appearance. Now Sydney must ask herself: is this the real Jim Lennox - or is his double?
When Sloane gets his hands on a terrifying Rimbaldi weapon that causes internal spontaneous combustion, Sydney must turn to a betrayed and hurt Dixon for help. But when her ex-partner refuses any assistance, She has no choice but to carry out the mission herself. When Sydney is captured, Vaughn must persuade Dixon to help the CIA rescue Sydney from an Afghan warlord's camp.
When Sydney learns that Vaughn is under investigation for being a double agent, Jack and Irina forge an unlikely partnership in their attempt to get their daughter out to the CIA for good. Kendall learns that Sark and Sloan are attempting to get their hands on a Rambaldi manuscript detailing the works of the human heart, so he sends Jack and Irina to Bangkok to learn more, and then to Panama to capture Sloan. But Irina betrays Jack and escapes from custody... this time for real.
Following her betrayal, the CIA try desperately to track down Irina Derevko. Their trail on Derevko leads them to Stuttgart and closer to Sark and Sloane, even as Sloane contemplates giving up his quest to complete Rambaldi's work in order to stay with his wife, Emily.
When the CIA intercepts a secret message, Sydney discovers that the life of Neil Caplan, the mathematician still held captive by Sloane and Irina, may be in danger from the most unlikely source: his wife Elsa whom Jack has arrested, forcing Sydney to try to clear Elsa's name by going on her own mission to Moscow and Spain to try to rescue Neil Caplan. Meanwhile, Sloane becomes obsessed with finding out who accidentally killed Emily, and Sark makes contact with the Francie impostor to locate the person responsible... by using Will to infiltrate the CIA satellite ...
As Dixon struggles with the death of his wife, He refuses to take time off from work until Sloane is brought to justice. But Sydney worries that Dixon's repressed rage could cause more harm that anything Sloane could do.
Sydney finds herself racing to clear Will's name when the Francie impostor frames him for the CIA intelligent leak by making him appear to be the other double of the Helix project. But Sark makes matters worse when he sends a team to extract Will, to make it look that he's guilty. Meanwhile across the globe, Irina and Sark discover a stumbling block could turn into an opportunity... with Sydney's cooperation.
Sydney must confront her mother, who tells a clue about "some Rambaldi artefacts" in Zurich, but it was a trap to capture Jack. As Sloane keeps the latter in hostage, Vaughn and Sydney go to Stockholm to capture Sark, who reveals the hideout in Mexico City. Meanwhile, Tippin discovers that Francie is in fact a "double" and is the one who framed him...
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...
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 ...
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 ...
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.